9PZF | pdb_00009pzf

Structure of KRAS G12C bound to Compound 4

PDB DOI: https://doi.org/10.2210/pdb9PZF/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-08-11 Released: 2026-03-11
Deposition Author(s): Kiefer, J.R., Wang, W., Oh, A., Yu, C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery and Characterization of Divarasib (GDC-6036), a Potent Covalent Inhibitor of KRAS G12C.

Endres, N.F., Do, S., Mroue, R., Terrett, J.A., Saabye, M., Oh, A., Hunsaker, T., Chan, E., Tran, J.C., Nguyen, L.K., Lian, Q., Ma, T.P., Garner, T., Gerosa, L., Beresini, M., Boudreau, A., Bronner, S.M., Cyr, P., Ishisoko, N., Izrayelit, Y., Jiang, F., Kellar, T., La, H., Labadie, S., Lardy, M., Liu, L., Liu, W., Miller, S., Rudolph, J., Plise, E., Sellers, B.D., Shao, C., Wang, W., Wang, Y., Wei, W., Wong, S., Yu, C., Yu, K., Yuen, P.W., Zang, R., Zhang, C., Zhou, Y., Zhu, X., Quinn, J.G., Ye, X., Kiefer, J.R., Mao, J., Evangelista, M., Merchant, M., Landry, M.L., Malhotra, S., Purkey, H.E.

(2026) J Med Chem 69: 5147-5165

PubMed: 41766690 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c02272
Primary Citation Related Structures:
9PZF, 9PZY

PubMed Abstract:
KRAS G12C is one of the most prevalent oncogenic mutations in nonsmall cell lung cancer. Herein we describe the discovery and optimization of divarasib (GDC-6036), an orally available, highly potent, and selective covalent KRAS G12C inhibitor. We demonstrate a significant noncovalent binding component of divarasib that contributes to its potency and rapid kinetics. Divarasib has greater potency and kinetics of alkylation compared with other KRAS G12C inhibitors in vitro and shows robust tumor growth inhibition in multiple KRAS G12C-positive cell lines.

Organizational Affiliation

Genentech, Inc., South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 44.62 kDa
Atom Count: 3,059
Modeled Residue Count: 338
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A, B	187	Homo sapiens	Mutation(s): 4 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CQ2 (Subject of Investigation/LOI) Query on A1CQ2 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	1-(4-{(7M)-7-[6-amino-3-(trifluoromethyl)pyridin-2-yl]-6-chloroquinazolin-4-yl}piperazin-1-yl)propan-1-one C₂₁ H₂₀ Cl F₃ N₆ O HYVDIXYPGCIEBX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]