9CZU

HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 9

• PDB DOI: https://doi.org/10.2210/pdb9CZU/pdb

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


• Deposited: 2024-08-05 Released: 2024-12-18 
• Deposition Author(s): Johnson, E., Mc Tigue, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Discovery of PF-07265028, A Selective Small Molecule Inhibitor of Hematopoietic Progenitor Kinase 1 (HPK1) for the Treatment of Cancer

Gallego, R.A., Cho-Schultz, S., Del Bel, M., Dechert-Schmitt, A.M., Donaldson, J.S., He, M., Jalaie, M., Kania, R., Matthews, J., McTigue, M., Tuttle, J.B., Risley, H., Zhou, D., Zhou, R., Ahmad, O.K., Bernier, L., Berritt, S., Braganza, J., Chen, Z., Cianfrogna, J.A., Collins, M., Costa Jones, C., Cronin, C.N., Davis, C., Dress, K., Edwards, M., Farrell, W., France, S.P., Grable, N., Johnson, E., Johnson, T.W., Jones, R., Knauber, T., Lafontaine, J., Loach, R.P., Maestre, M., Miller, N., Moen, M., Monfette, S., Morse, P., Nager, A.R., Niosi, M., Richardson, P., Rohner, A.K., Sach, N.W., Timofeevski, S., Tucker, J.W., Vetelino, B., Zhang, L., Nair, S.K.

(2024) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.4c01930

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.96 kDa 
• Atom Count: 9,827 
• Modelled Residue Count: 1,139 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase kinase 1	A, B, C, D	309	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A1D (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth C], I [auth D]	6-methoxy-4-[(methylamino)methyl]-2-(6-{4-[(2S)-4,4,4-trifluorobutan-2-yl]-4H-1,2,4-triazol-3-yl}pyridin-2-yl)-2,3-dihydro-1H-isoindol-1-one C22 H23 F3 N6 O2 DVPICGLUATZNJY-ZDUSSCGKSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.19	α = 67.33
b = 84.26	β = 73.51
c = 87.32	γ = 76.15

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
BUSTER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Johnson, E., Mc Tigue, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release