7KAC | pdb_00007kac

Crystal structure of HPK1 (MAP4K1) kinase in complex with 5-{[4-{[(1S)-2-HYDROXY-1-PHENYLETHYL]AMINO}-5-(1,3,4-OXADIAZOL-2-YL)PYRIMIDIN-2-YL]AMINO}-3,3-DIMETHYL-2-BENZOFURAN-1(3H)-ONE

• PDB DOI: https://doi.org/10.2210/pdb7KAC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2020-09-30 Released: 2021-01-13 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.232 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Using yeast surface display to engineer a soluble and crystallizable construct of hematopoietic progenitor kinase 1 (HPK1).

Lau, W.L., Pearce, B., Malakian, H., Rodrigo, I., Xie, D., Gao, M., Marsilio, F., Chang, C., Ruzanov, M., Muckelbauer, J.K., Newitt, J.A., Lipovsek, D., Sheriff, S.

(2021) Acta Crystallogr F Struct Biol Commun 77: 22-28

• PubMed: 33439152 
• DOI: https://doi.org/10.1107/S2053230X20016015
• Primary Citation Related Structures: 
  7KAC


• PubMed Abstract: 
  

  Hematopoietic progenitor kinase 1 (HPK1) is an intracellular kinase that plays an important role in modulating tumor immune response and thus is an attractive target for drug discovery. Crystallization of the wild-type HPK1 kinase domain has been hampered by poor expression in recombinant systems and poor solubility. In this study, yeast surface display was applied to a library of HPK1 kinase-domain variants in order to select variants with an improved expression level and solubility. The HPK1 variant with the most improved properties contained two mutations, crystallized readily in complex with several small-molecule inhibitors and provided valuable insight to guide structure-based drug design. This work exemplifies the benefit of yeast surface display towards engineering crystallizable proteins and thus enabling structure-based drug discovery.

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Organizational Affiliation: 
• Biologics Discovery, Bristol-Myers Squibb Research and Development, 100 Binney Street, Cambridge, MA 02142, USA.
Molecular Structure and Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA.
Protein Science, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA.
Molecular Structure and Design, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.02 kDa 
• Atom Count: 4,247 
• Modeled Residue Count: 571 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Mitogen-activated protein kinase kinase kinase kinase 1	A, B	340	Homo sapiens	Mutation(s): 2  Gene Names: MAP4K1, HPK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens) Explore Q92918  Go to UniProtKB:  Q92918
PHAROS:  Q92918 GTEx:  ENSG00000104814

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W9D (Subject of Investigation/LOI)	C [auth A], D [auth B]	5-{[4-{[(1S)-2-hydroxy-1-phenylethyl]amino}-5-(1,3,4-oxadiazol-2-yl)pyrimidin-2-yl]amino}-3,3-dimethyl-2-benzofuran-1(3H)-one C24 H22 N6 O4 RVSSNRBUPQUIEG-LJQANCHMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.232 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.83	α = 78.81
b = 58.47	β = 79.82
c = 60.48	γ = 66.08

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
AMoRE	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Sheriff, S.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description