Case 1:19-cv-01681-CFC-SRF Document 55 Filed 08/10/20 Page 163 of 415 PageID #: 2543
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`
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`
`
`
`
`Civil Action No. 19-1681-CFC
`
`
`
`
`) ) ) ) ) ) ) ) ) ) ) ) )
`
`
`
`THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF
`NEW YORK and QIAGEN
`SCIENCES, LLC,
`
`
`Plaintiffs,
`
`
`v.
`
`
`ILLUMINA, INC.,
`
`
`Defendant.
`
`
`
`
`
`
`
`
`
`DECLARATION OF JOHN KURIYAN, PH.D. IN SUPPORT OF
`PLAINTIFFS’ OPENING CLAIM CONSTRUCTION BRIEF
`
`
`
`
`
`
`
`
`
`JA0157
`
`IPR2020-00988 Exhibit Page 1
`
`Columbia Ex. 2037
`Illumina, Inc. v. The Trustees
`of Columbia University
`in the City of New York
`IPR2020-01177
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 55 Filed 08/10/20 Page 164 of 415 PageID #: 2544
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`
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`TABLE OF CONTENTS
`
`I.
`
`I.
`
`II.
`
`II.
`
`Professional Experience and Qualifications ........................................................................2
`
`Prior Expert Testimony ........................................................................................................4
`
`Compensation ......................................................................................................................4
`
`Materials Considered ...........................................................................................................4
`
`III.
`
`Scope of Testimony .............................................................................................................5
`
`IV.
`
`Level of Ordinary Skill in the Art ........................................................................................5
`
`V.
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`Meaning of “Diameter”........................................................................................................6
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`- i -
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`JA0158
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`IPR2020-00988 Exhibit Page 2
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`I.
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`Professional Experience and Qualifications
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`1.
`
`I am Professor and Howard Hughes Medical Institute investigator
`
`in the Department of Molecular and Cell Biology at the University of California,
`
`Berkeley, California. I am also a Professor in the Department of Chemistry at
`
`Berkeley. I joined the faculty of the University of California, Berkeley in 2001. I
`
`have been a Howard Hughes Medical Institute investigator since 1990. I am also
`
`a faculty scientist at Lawrence Berkeley National Laboratory, Berkeley, California
`
`(2001 to present).
`
`2.
`
`Prior to the appointments in Berkeley, I was a Professor at The
`
`Rockefeller University, New York, New York (1987-2001). From 1993 to 2001, I
`
`was also the Patrick E. and Beatrice Haggerty Professor at the Rockefeller
`
`University.
`
`3.
`
`I received my Ph.D. in Chemistry in 1986 from the Massachusetts
`
`Institute of Technology, Cambridge, Massachusetts. I was a post-doctoral fellow
`
`from 1986 to 1987 at Harvard University, Cambridge, Massachusetts.
`
`4.
`
`I received my Bachelor of Science degree in Chemistry from
`
`Juniata College, Huntington, Pennsylvania in 1981. I also attended the University
`
`of Madras from 1977 to 1979.
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`- 2 -
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`JA0159
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`IPR2020-00988 Exhibit Page 3
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`5.
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`I have extensive experience in the fields of molecular biology,
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`biochemistry and structural biology. My laboratory’s focus is on the structure and
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`function of proteins involved in cellular signal transduction and DNA replication.
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`My laboratory utilizes x-ray crystallography and electron microscopy, as well as
`
`biochemical, biophysical, and computational analyses to understand how various
`
`proteins function.
`
`6.
`
`My research mainly focuses on the atomic-level structure and
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`mechanism of the enzymes and molecular switches that carry out critical cellular
`
`regulatory processes, using x-ray crystallography and electron microscopy to
`
`determine the three-dimensional structures of proteins involved in those processes,
`
`as well as biochemical, biophysical, and cell biological analyses to elucidate
`
`protein mechanisms of action. One area of my special expertise involves the
`
`molecular structure of DNA polymerases.
`
`7.
`
`Research in my laboratory has resulted in fundamental
`
`contributions to understanding the structural basis for high-speed DNA
`
`replication. Other breakthroughs include determining the auto-inhibited structures
`
`of several tyrosine kinases, including Src family kinases and elucidating the
`
`mechanism of allosteric activation of the kinase domains of the EGF receptor,
`
`- 3 -
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`JA0160
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`IPR2020-00988 Exhibit Page 4
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`which have provided new insights that directly resulted in the development of
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`novel therapies used in cancer and immune diseases.
`
`8.
`
`My curriculum vitae, which describes in greater detail my
`
`professional experience and qualifications, is attached as Exhibit 1 (JA0176–94).
`
`I.
`
`Prior Expert Testimony
`
`9.
`
`During the preceding five years, I have not testified at deposition
`
`or at trial.
`
`II. Compensation
`
`10.
`
`I am being compensated for my work in connection with this
`
`litigation at my rate of $650 per hour for the time I spend working on this matter.
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`II. Materials Considered
`
`11.
`
`The opinions and conclusions I express in this report are based on
`
`my review of the patents-in-suit, U.S. Patent Nos. 10,407,458 (“’458 Patent”),
`
`10,407,459 (“’459 Patent’”), 10,435,742 (“’742 Patent”), 10,457,984 (“’984
`
`Patent”) and 10,428,380 (“’380 Patent”); portions of the prosecution file histories
`
`of those patents (“prosecution history”) that relate to the size of the capping
`
`groups; and materials listed in Exhibit 2 (JA0195–96).
`
`12.
`
`My opinions and conclusions are also based on (1) my general
`
`knowledge of protein chemistry, structural biology and biochemistry, (2) my
`
`- 4 -
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`JA0161
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`IPR2020-00988 Exhibit Page 5
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`experience and training as a scientist, consultant, and advisor in the biotech
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`industry as it relates to discovery and development of new medicines, and (3) my
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`experience working with others in the fields of chemistry, molecular biology,
`
`biochemistry and structural biology that provides me insight as to the thinking of a
`
`person of ordinary skill, as set forth below.
`
`III. Scope of Testimony
`
`13.
`
`I have been asked to provide my opinion on the meaning of
`
`“diameter” as used in the prosecution history, particularly in view of the diameter
`
`measurements listed in the prosecution history. Specifically, I have been asked
`
`whether the diameter of the chemical groups discussed in the prosecution history
`
`as being less than 3.7 Å in diameter would be understood by a person of ordinary
`
`skill in the art to correspond to their widths or lengths.
`
`14.
`
`For the reasons set forth below, it is my opinion that a person of
`
`ordinary skill in the art would readily understand that diameter refers to width, not
`
`length (or longest dimension) of each chemical group.
`
`IV. Level of Ordinary Skill in the Art
`
`15.
`
`For the subject matter of the patents-in-suit, it is my opinion that
`
`the person of ordinary skill in the relevant time period (October 6, 2000) would
`
`have a Ph.D. in chemistry, structural biology, biochemistry, molecular biology or
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`- 5 -
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`JA0162
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`IPR2020-00988 Exhibit Page 6
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`a closely-related discipline, as well as two or more years of experience with DNA
`
`sequencing technology.
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`16.
`
`My opinions provided herein are based on an interpretation of
`
`diameter as understood by a person of ordinary skill in the art.
`
`V. Meaning of “Diameter”
`
`17.
`
`I understand that the parties have submitted proposed claim
`
`constructions on the term “small” as used in the claims of the patents-in-suit, and
`
`that the proposed constructions are as follows:
`
`Claims
`
`’458 Patent: Claims 1, 2
`
`’459 Patent: Claims 1, 2
`
`’742 Patent: Claims 1, 2
`
`’984 Patent: Claims 1, 2
`
`’380 Patent: Claims 1, 3
`
`
`
`Plaintiffs’ Proposed
`Construction
`
`“A chemical group
`that has a diameter,
`i.e., width, that is
`less than 3.7Å”
`
`Defendant’s
`Proposed
`Construction
`
`“A chemical group
`that fits within the
`rat DNA
`polymerase active
`site shown in Fig. 1
`of the patent, i.e.
`has a longest
`dimension less than
`3.7Å, including the
`3′ oxygen”
`
`18.
`
`I understand that the parties agree that “small” means a chemical
`
`group having a dimension less than 3.7 Å.
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`- 6 -
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`JA0163
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`IPR2020-00988 Exhibit Page 7
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`

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`19.
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`I have been advised that the parties disagree as to which
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`dimension of the chemical group must be less than 3.7 Å. Plaintiffs assert that the
`
`dimension is “diameter, i.e., width,” whereas, defendant argues that it must be the
`
`“longest dimension . . . including the 3’ oxygen” (i.e., length).
`
`20.
`
`As explained below, it is my opinion, that a person of ordinary
`
`skill reading the patent specification and prosecution history would readily
`
`understand that the “diameter” of the chemical group, as that term is used in the
`
`prosecution history, is the width of the chemical group and cannot be “the longest
`
`dimension . . . including the 3’ oxygen”.
`
`21.
`
`The patent specification explains that the chemical groups used to
`
`cap the 3’ oxygen of the nucleotide ribose (“3’-O”) must be small. The
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`specification provides two examples of small chemical groups, MOM (–CH2-
`
`OCH3) and allyl (–CH2-CH=CH2). (‘458 Patent (JA0011 at 3:41-42).) Thus, a
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`person of ordinary skill would understand that MOM and allyl meet the size
`
`requirement for a small chemical group.
`
`22.
`
`The meaning of a small chemical group is further discussed in the
`
`prosecution history of the patents. Specifically, a Declaration submitted by Dr. Ju,
`
`a named inventor, explains that, based on the disclosures in the patents-in-suit, a
`
`person of ordinary skill would have understood that the chemical group capping
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`- 7 -
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`JA0164
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`IPR2020-00988 Exhibit Page 8
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`the 3’-O had to be less than 3.7 Å in “diameter” to fit within the active site of the
`
`benchmark polymerase discussed in the specification. The Declaration also
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`explains that the two exemplified groups, MOM and allyl, had diameters that were
`
`less than 3.7 Å. (’458 Patent PH, 5/9/19 Supplemental Communication at 4
`
`(JA0031); Ju Decl. (JA0062–64 at ¶¶ 10-18).)
`
`23.
`
`In addition, accompanying the Declaration is an “Analysis”
`
`section that provides additional details on the meaning of diameter, as it applies to
`
`small chemical groups. (‘458 Patent FH, Ju Decl., Ex. C (JA0082–84)).
`
`Specifically, the Analysis gives the diameters for specific chemical groups, as
`
`follows:
`
`24.
`
`Based on the prosecution history, including those listed
`
`
`
`dimensions, a person of ordinary skill would have understood that the “diameter”
`
`of a small chemical group is the width of the chemical group (Plaintiffs’
`
`construction) and not its longest dimension (Defendant’s construction).
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`- 8 -
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`JA0165
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`IPR2020-00988 Exhibit Page 9
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`25.
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`The widths and lengths of chemical groups are derived from the
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`lengths and angles of the bonded atoms in the group, which are reported in
`
`chemical treatises (e.g., STEREOCHEMISTRY OF ORGANIC COMPOUNDS –
`
`PRINCIPLES AND APPLICATIONS, Nasipuri, D., Revised 2nd Ed., New Age
`
`International Publishers, 1994 (JA0198–212); Nielsen and Sjögren, The
`
`Vibrational Spectra, Molecular Structure and Conformation of Organic Azides.
`
`Part IV, J. Mol. Struct. (Theochem), 150:361-379, 1987 (JA0214–32). Chemical
`
`bond lengths and angles are fundamental chemical properties that do not change.
`
`A person of ordinary skill, well before 2000, would have been able to ascertain
`
`those values without trouble for at least two reasons.
`
`26.
`
`First, the calculations of molecular dimensions can be made
`
`manually based on the lengths and angles of the bonds in the chemical groups,
`
`which information is provided in references dating back over 50 years. Indeed, a
`
`person of ordinary skill would have been able to arrive at estimates of the lengths
`
`of the listed chemical groups without performing precise manual calculations,
`
`based on that person’s knowledge of atom sizes. Those length estimations would
`
`clearly exceed the diameter values listed in the Analysis.
`
`27.
`
`Second, since well before 2000, chemical graphics programs have
`
`been available and used to calculate the lengths and widths of chemical groups.
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`These programs all use the same underlying principles and properties (e.g., bond
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`- 9 -
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`JA0166
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`IPR2020-00988 Exhibit Page 10
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`angles and bond lengths) to arrive at the same end results as a manual calculation.
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`These calculations would be the same regardless of the software package used to
`
`make the calculations, as they are all based on chemical principles that do not
`
`change.
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`28.
`
`As disclosed in the prosecution history, Dr. Ju used such software
`
`to determine the diameters of the various chemical groups listed above. (’458
`
`Patent PH, Ju Decl. (JA0063–64 at ¶¶ 16-17).)
`
`29.
`
`I was asked to determine the widths and lengths of the four groups
`
`identified in the prosecution history as having diameters less than 3.7 Å. To do
`
`this, I used PyMOL, a commercially available and widely used software package
`
`to display the structure of each capping group (with each group attached to
`
`oxygen for purposes of making the various measurements discussed below). In
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`doing so, I used the formulae and structures of the allyl, MOM, methylthiomethyl,
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`and azidomethyl chemical groups reproduced in the patent prosecution history
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`(’458 Patent PH, Ju Decl., Ex. C, p.3 (JA0084)). For example, for the allyl
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`chemical group I used the software PRODRG (A.W. Schuttelkopf and D.M.F. van
`
`Aalten (2004) Acta Crystallograph. D60, 1355-1363), available on a website, to
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`specify the structure O-CH2-CH=CH2 which the software converts into a format
`
`for viewing by PyMOL. The dimensions of the group would be determined by
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`selecting the farthest opposing atoms in the length and width dimensions. As
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`- 10 -
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`JA0167
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`IPR2020-00988 Exhibit Page 11
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`stated above, the software calculates the distance between those selected atoms
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`using the fundamental chemical principles of bond lengths and angles.
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`30.
`
`I created an illustration showing the length and width dimensions
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`of the allyl chemical group. In making the illustration I first reproduced the 2-
`
`dimensional (“2-D”) structure of 3’-O-allyl-dCTP nucleotide from the prosecution
`
`history (’458 Patent PH, Ju Decl., Ex. C, p.3 (JA0084)). I then drew the 3’-O-
`
`allyl chemical group portion of the nucleotide, indicated by the dashed circle in
`
`the 2-D drawing, in 3-D, displaying the group in the ball and stick format. In the
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`3-D rendering, the red represents the oxygen atom attached to the 3’ carbon of the
`
`nucleotide. The green represents the three carbon atoms of the allyl chemical
`
`group shown in the 2-D drawing. The white represents the hydrogen atoms that
`
`are attached to the carbon atoms. Hydrogen atoms are typically not shown in 2-D
`
`chemical drawings, but their positions are defined based on chemical principles.
`
`31.
`
`When employing the chemical graphics program, the skilled
`
`artisan is able to view the chemical group in three dimensions, rotating the
`
`structure in space to observe the lengths and widths of the groups from different
`
`perspectives. The illustrations below, presented necessarily in two dimensions,
`
`provide a single perspective for each chemical group, which allows the lengths
`
`and widths to be viewed together. Regardless of the perspective displayed, each
`
`chemical group has a length dimension, which is the group’s longest dimension,
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`- 11 -
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`JA0168
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`IPR2020-00988 Exhibit Page 12
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`and a dimension substantially perpendicular to the length dimension, which is the
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`chemical group’s widest (i.e., width) dimension.
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`32.
`
`As shown in the illustration below, the allyl chemical group has a
`
`length of 4.6 Å from the 3’ oxygen (from A to B, indicated by the horizontal line),
`
`and a width of 3.1 Å, (from C to D, indicated by the vertical line), with or without
`
`a 3’ oxygen.
`
`
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`
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`33.
`
`I followed the same format for illustrating each of the other
`
`chemical groups disclosed in the prosecution history. As shown in the illustration
`
`below, the methoxymethyl (MOM) chemical group, has a length of 4.4 Å from the
`
`
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`- 12 -
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`JA0169
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`IPR2020-00988 Exhibit Page 13
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`3’ oxygen (from A to B, indicated by the horizontal line), and a width of 2.1 Å
`
`(from C to D, indicated by the vertical line), with or without a 3’ oxygen.
`
`
`
`34.
`
`As shown in the illustration below, the methylthiomethyl
`
`chemical group has a length of 4.9 Å from the 3’ oxygen (from A to B, indicated
`
`by the horizontal line), and a width of 2.4 Å (from C to D, indicated by the
`
`vertical line), with or without a 3’ oxygen. In this drawing, yellow represents a
`
`sulfur atom.
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`- 13 -
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`JA0170
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`IPR2020-00988 Exhibit Page 14
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`35.
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`As shown in the illustration below, the azidomethyl chemical
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`group has a length of 4.9 Å from the 3’ oxygen (from A to B, indicated by the
`
`horizontal line), and a width of 2.1 Å (from C to D, indicated by the vertical line),
`
`with or without a 3’ oxygen. In this drawing, blue represents nitrogen atoms.
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`- 14 -
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`JA0171
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`IPR2020-00988 Exhibit Page 15
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`36.
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`My measurements, along with the listed diameters from the
`
`prosecution history (highlighted in yellow), are summarized in tabular form
`
`below.
`
`Chemical Group Diameter in the
`prosecution
`history
`3.0 Å
`
`Allyl
`
`Measured width1 Measured longest
`dimension (from
`the 3’ oxygen)
`4.6 Å
`
`3.1 Å
`
`MOM
`
`2.1 Å
`
`Methylthiomethyl
`
`2.4 Å
`
`Azidomethyl
`
`2.1 Å
`
`2.1 Å
`
`2.4 Å
`
`2.1 Å
`
`4.4 Å
`
`4.9 Å
`
`4.9 Å
`
`
`1 The measured width is the same regardless of whether or not the oxygen is
`included, as the oxygen adds only to the length dimension.
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`- 15 -
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`JA0172
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`IPR2020-00988 Exhibit Page 16
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`37.
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`As can be seen, the widths that a person of ordinary of skill would
`
`have obtained consistently match (with a minor deviation for the allyl, possibly
`
`due to rounding) with the listed diameters in the inventor’s Declaration. As can
`
`also be seen, none of the lengths/longest dimensions obtained matches the stated
`
`diameters in the inventor’s Declaration. Indeed, the lengths are much larger than
`
`the diameter values provided in the Declaration. Therefore, a person of ordinary
`
`skill at the time would have readily understood that the “diameter” of the chemical
`
`groups cannot be its longest dimension as that measurement exceeds the
`
`“diameters” of the chemical groups provided in the prosecution history. Instead,
`
`diameter clearly refers to the width, which matches the diameters listed in the
`
`prosecution history. (’458 Patent PH, Ju Decl., Ex. C, p.3 (JA0084).) A person of
`
`ordinary skill would have arrived at this conclusion by calculating the dimensions
`
`manually or by using software existing at the time.
`
`38.
`
`Moreover, Defendant’s understanding of the relevant
`
`measurement—that the diameter would refer to the “longest dimension . . .
`
`including the 3’ oxygen”—would exclude the chemical groups designated as
`
`small in the patent specification. Specifically, the patent identifies both allyl and
`
`MOM as being embodiments of the invention (i.e., small chemical groups). Under
`
`Defendant’s proposal of using the longest dimension of these chemical groups
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`- 16 -
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`JA0173
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`IPR2020-00988 Exhibit Page 17
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`(including the 3’ oxygen) as the relevant measurement, those two embodiments
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`would far exceed 3.7 Å, and consequently, be excluded from the meaning of a
`
`small chemical group. Given that the patent identifies those groups explicitly as
`
`representative of suitably small chemical groups, a person of ordinary skill would
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`disagree with that conclusion.
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`- 17 -
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`JA0174
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`IPR2020-00988 Exhibit Page 18
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`39.
`
`I declare under penalty of perjury that the foregoing is true and
`
`correct.
`
`
`Executed on: June 1, 2020 ____________________________
`
`
`
`
`
` John Kuriyan, Ph.D.
`
`
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`JA0175
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`IPR2020-00988 Exhibit Page 19
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`Case 1:19-cv-01681-CFC-SRF Document 55 Filed 08/10/20 Page 182 of 415 PageID #: 2562
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`Exhibit 1
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`JA0176
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`IPR2020-00988 Exhibit Page 20
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`Case 1:19-cv-01681-CFC-SRF Document 55 Filed 08/10/20 Page 183 of 415 PageID #: 2563
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`John Kuriyan, curriculum vitae, June 1, 2020
`
`John Kuriyan
`
`Date of Birth:
`
`Citizenship: USA
`
`July 24, 1960
`
`Place of Birth: Mavelikera, Kerala, India
`
`Present Position:
`Professor
`
`
`University of California, Berkeley
`
`Department of Molecular and Cell Biology
`
`Department of Chemistry
`
`Investigator, Howard Hughes Medical Institute
`
`
`Mailing and Contact Information:
`Molecular & Cell Biology
`176 Stanley Hall, MC 3220
`University of California, Berkeley
`Berkeley, CA 94720-322
`
`Phone: 510 643 0137
`E-mail: kuriyan@berkeley.edu
`
`Education:
`1.
`
`2.
`
`3.
`
`Positions:
`1.
`
`2.
`
`3.
`
`4.
`
`5.
`
`6.
`
`7.
`8.
`
`(transferred after two years at the University of Madras, India).
`
`Juniata College, Huntingdon, Pennsylvania. 1981. B.S., Chemistry;

`Massachusetts Institute of Technology, Cambridge, MA.

`Department of Chemistry. Ph. D. (Physical Chemistry) February 1986. 

`
`Supervisors: Gregory A. Petsko and Martin Karplus (Harvard University).
`Title of Thesis: The Structure and Flexibility of Myoglobin: Molecular
`Dynamics and X-ray Crystallography.
`Harvard University, Cambridge, MA. March 1986 - May 1987.
`Department of Chemistry. Post-doctoral Fellow with Professors Martin
`Karplus and Gregory A. Petsko (MIT).
`
`June 1987 - February 1992: Assistant Professor. The Rockefeller
`University, New York, NY.
`March 1992 - March 1993: Associate Professor. The Rockefeller
`University, New York, NY.
`April 1993 - June 1997: Professor. The Rockefeller University, New York,
`NY.
`July 1997 - July 2001: Patrick E. and Beatrice M. Haggerty Professor.
`The Rockefeller University, New York, NY.
`November 1995 - June 1997. Associate Dean of Graduate Studies, The
`Rockefeller University, New York, NY.
`September 1990 - August 1993: Assistant Investigator. Howard Hughes
`Medical Institute.
`August 1993 – present: Investigator, Howard Hughes Medical Institute.
`July 2001 – present. Professor of Molecular and Cell Biology and
`Chemistry. University of California, Berkeley.
`
`JA0177
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`John Kuriyan, curriculum vitae, June 1, 2020
`
`9.
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`10.
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`11.
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`July 2001- September 2004: Divisional Deputy for Structural Biology at
`the Advanced Light Source, Physical Biosciences Division. Lawrence
`Berkeley National Laboratory.
`September 2004 - present: Faculty Scientist, Physical Biosciences
`Division, Lawrence Berkeley National Laboratory.
`July 2007 – December 2012. Head, Division of Biochemistry and
`Molecular Biology, Department of Cell and Molecular Biology, University
`of California, Berkeley.
`
`Selected Honors:
`
`Member, US National Academy of Medicine, 2018
`Stein & Moore Award, The Protein Society, 2017
`Foreign Member of The Royal Society, London. Elected April 2015.
`Doctor of Humane Letters, honoris causa, Juniata College, Huntington, PA. May 2014.
`Merck Award, American Society of Biochemistry and Molecular Biology, 2009.
`Fellow, American Academy of Arts and Sciences, Elected 2008.
`Richard Lounsbery Award, US National Academy of Sciences, 2005.
`Member, US National Academy of Sciences, Elected 2001.
`Eli Lilly Award of the American Chemical Society, 1998.
`DuPont-Merck Award of the Protein Society, 1997.
`Schering-Plough Award of the American Society of Biochemistry & Molecular Biology,
`1994.
`Pew Scholar in the Biomedical Sciences, 1989-1993.
`
`2.
`
`3.
`4.
`5.
`
`6.
`
`7.
`
`8.
`
`9.
`
`Professional Service (selected)
`BBCA (Biophysical Chemistry) study section, National Institutes of Health,

`1.
`Ad hoc member, 1991. Charter Member, 1995 - 1999.
`Member, Standing Advisory Committee (Overseas), Department of
`Biotechnology, Government of India, 1997-2001.
`Member, Board of Scientific Counselors, National Cancer Institute, 2001-2005.
`Member, Board of Trustees, Juniata College, Huntingdon, PA. 2004-2007.
`Member, Scientific Management Board, National Center for Biological Sciences,
`Tata Institute of Fundamental Research, Bangalore, July 2006-present.
`Member, Board of Scientific Advisors, Jane Coffin Childs Memorial Fund, July
`2007-2014.
`Member, National Advisory Committee, Pew Scholars Program in the
`Biomedical Sciences. 2007 – present.
`Member, Advisory Committee, Burroughs Wellcome Fund Career Awards at the
`Scientific Interface. 2007–2015.
`Editorial Board, FEBS J. (formerly European Journal of Biochemistry),
`2000-2008.
`Editor, Advances in Protein Chemistry, 2001-2009.
`Associate Editor, Cell. 1995-2012.
`Member, Editorial Board, Proceedings of the National Academy of Sciences
`(USA). 2005- present.
`Co-Head of Structural Biology Faculty (with David Eisenberg), Faculty of 1000,
`2001-2012.
`Senior Editor, eLife. 2012-present.
`Scientific Advisory Board, Skirball Institute, NYU Medical Center. 2013 - present.
`Member, Committee on Budget and Interdepartmental Relations, University of
`California, Berkeley. 2015 – 2017.
`Member, Scientific Advisory Board, Amgen. 2016 – present.
`
`10.
`11.
`12.
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`13.
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`14.
`15.
`16.
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`17.
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`JA0178
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`Case 1:19-cv-01681-CFC-SRF Document 55 Filed 08/10/20 Page 185 of 415 PageID #: 2565
`
`John Kuriyan, Bibliography. June 1, 2020
`
`
`1.
`Bhattacharyya, M, Lee, YK, Muratcioglu, S, Qiu, B, Nyayapati, P, Schulman, H.,
`Groves, JT, Kuriyan J (2020). Flexible linkers in CaMKII control the balance between
`activating and inhibitory autophosphorylation. eLife, 9. http://doi.org/10.7554/eLife.53670
`PMID: 32149607
`2.
`Bhattacharyya M, Karandur D, Kuriyan J (2019) Structural Insights into the
`Regulation of Ca2+/Calmodulin-Dependent Protein Kinase II (CaMKII). Cold Spring Harb
`Perspect Biol. pii: a035147. doi: 10.1101/cshperspect.a035147. [Epub ahead of print]
`PMID: 31653643
`3.
`Lo WL, Shah NH, Rubin SA, Zhang W, Horkova V, Fallahee IR, Stepanek O, Zon
`LI, Kuriyan J, Weiss A (2019) Slow phosphorylation of a tyrosine residue in LAT
`optimizes T cell ligand discrimination. Nat Immunol. 2019 Oct 14. doi: 10.1038/s41590-
`019-0502-2. [Epub ahead of print]. PMID: 31611699
`4.
`Kondo Y, Ognjenović J, Banerjee S, Karandur D, Merk A, Kulhanek K, Wong K,
`Roose JP, Subramaniam S, Kuriyan J (2019) Cryo-EM structure of a dimeric B-Raf:14-3-
`3 complex reveals asymmetry in the active sites of B-Raf kinases. Science 366:109-115.
`PMID: 31604311
`5.
`McSpadden ED, Xia Z, Chi CC, Susa AC, Shah NH, Gee CL, Williams ER, Kuriyan
`J (2019) Variation in assembly stoichiometry in non-metazoan homologs of the hub
`domain of Ca2+/Calmodulin-dependent protein kinase II Protein Sci. 28: ;28(6):1071-
`1082. doi: 10.1002/pro.3614. Epub 2019 Apr 17. PMID: 30942928
`6.
`Simonetta KR, Taygerly J, Boyle K, Basham SE, Padovani C, Lou Y, Cummins TJ,
`Yung SL, von Soly SK, Kayser F, Kuriyan J, Rape M, Cardozo M, Gallop MA, Bence NF,
`Barsanti PA, Saha A. (2019) Prospective discovery of small molecule enhancers of an
`E3 ligase-substrate interaction. Nat Commun. 2019 Mar 29;10(1):1402. doi:
`10.1038/s41467-019-09358-9. PMID: 30926793
`7.
`Shah NH, Kuriyan J (2019) “Understanding molecular mechanisms in cell signaling
`through natural and artificial sequence variation” Nat Struct Mol Biol. 26:25-34. doi:
`10.1038/s41594-018-0175-9. PMID: 30598552
`8.
`Huang WYC, Alvarez S, Kondo Y, Lee YK, Chung JK, Lam HYM, Biswas KH,
`Kuriyan J, Groves JT (2019) “A molecular assembly phase transition and kinetic
`proofreading modulate Ras activation by SOS”, Science, 363:1098-1103. PMID:
`30846600
`9.
`Chung, JK, Nocka, LM, Wang, Q, Kadlecek, TA, Weiss, A, *Kuriyan, J, *Groves, JT
`(2019) “Switch-like activation of Bruton’s tyrosine kinase by membrane-mediated
`dimerization,” Proc Natl Acad Sci U S A. May 28;116(22):10798-10803. doi:
`10.1073/pnas.1819309116. Epub 2019 May 10. PMID:31076553 PMCID: PMC6561188
`10.
`Shah NH, Amacher JF, Nocka LM, Kuriyan J (2018) “The Src module: an ancient
`scaffold in the evolution of cytoplasmic tyrosine kinases” Crit Rev Biochem Mol Biol.
`53:535-563. doi:10.1080/10409238.2018.1495173. PMID: 30183386
`11.
`Lo WL, Shah NH, Ahsan N, Horkova V, Stepanek O, Salomon AR, Kuriyan J,
`Weiss A (2018) Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70
`to LAT. Nat Immunol. 2018 Jul;19(7):733-741. PMCID: PMC6202249 PMID: 29915297
`12.
`Bandaru, P, Kondo, Y, *Kuriyan, J. (2018) “The interdependent activation of Son-
`of-Sevenless and Ras”, Cold Spring Harb Perspect Med doi:
`10.1101/cshperspect.a031534 PMID: 29610148
`13. Cantor, AJ, Shah, NH and *Kuriyan, J (2018) “Deep mutational analysis reveals
`functional trade-offs in the sequences of EGFR autophosphorylation sites,” Proc Natl
`
`Page 1 of 16
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`John Kuriyan, Bibliography. June 1, 2020
`
`Acad Sci U S A. 2018 Jul 31;115(31):E7303-E7312. doi:10.1073/pnas.1803598115.
`PMID: 30012625, PMCID: PMC6077704
`14.
`Shah, NH, Löbel, M, Weiss, A, *Kuriyan, J (2018) “Fine-tuning of substrate
`preferences of the Src-family kinase Lck revealed through a high-throughput specificity
`screen,” eLife, 7. doi: 10.7554/eLife.35190. PMID: 29547119 PMCID: PMC5889215
`PMID: 29547119
`15.
`Amacher, JF, Hobbs, HT, Cantor, AC, Shah, L, Rivero, M-J, Mulchand, SA,
`*Kuriyan, J (2018) “Phosphorylation control of the ubiquitin ligase cbl is conserved in
`choanoflagellates.,” Protein Science. 27(5):923-932 doi: 10.1002/pro.3397. PMID:
`29498112. PMCID: PMC5916117
`16.
`Vercoulen, Y, Kondo, Y, Iwig, JS, Janssen, A, White, KA, Amini, M, Barber, DL,
`*Kuriyan, J, *Roose, JP (2017) “A histidine pH sensor regulates activation of the Ras-
`specific guanine nucleotide exchange factor RasGRP1.,” eLife, 6. doi:
`10.7554/eLife.29002.
`17.
`Karandur, D, Nawrotek, A, *Kuriyan, J and *Cherfils, J (2017) “Multiple interactions
`between an Arf/GEF complex and charged lipids determine activation kinetics on the
`membrane.,” Proceedings of the National Academy of Sciences of the United States of
`America, 114(43), pp. 11416–11421. doi: 10.1073/pnas.1707970114.
`18.
`Courtney, AH, Amacher, JF, Kadlecek, T A, Mollenauer, M N., Au-Yeung, B B,
`Kuriyan, J and *Weiss, A (2017) “A Phosphosite within the SH2 Domain of Lck
`Regulates Its Activation by CD45,” Molecular Cell, 67(3), p 498–511.e6.
`doi:10.1016/j.molcel.2017.06.024.
`19.
`Bandaru, P, Shah, NH, Bhattacharyya, M, Barton, JP, Kondo, Y, Cofsky, JC, Gee,
`CL, Chakraborty, AK, Kortemme, T, *Ranganathan, R, *Kuriyan, J (2017)
`“Deconstruction of the Ras switching cycle through saturation mutagenesis.,” eLife, 6.
`doi:10.7554/eLife.27810.
`20.
`Visperas PR, Wilson CG, Winger JA, Yan Q, Lin K, Arkin MR, Weiss A, *Kuriyan J
`(2017) Identification of Inhibitors of the Association of ZAP-70 with the T Cell Receptor
`by High-Throughput Screen. SLAS Discovery, 22:324-331. PMID: 27932698
`21.
`Huang Y, Bharill S, Karandur D, Pete