9HMR | pdb_00009hmr

KRAS-G12V-D92C covalently bound to BI-1830

PDB DOI: https://doi.org/10.2210/pdb9HMR/pdb

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

Deposited: 2024-12-09 Released: 2025-12-24
Deposition Author(s): van Tienen, L.M., Zak, K.M., Kessler, D., Sellers, W.R.
Funding Organization(s): European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.205 (Depositor), 0.209 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Systematic Cysteine-Scanning Identifies a Druggable Pocket in Oncogenic KRAS

van Tienen, L.M., Sellers, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 80.84 kDa
Atom Count: 5,578
Modeled Residue Count: 618
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A, B, C, D	170	Homo sapiens	Mutation(s): 5 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	E [auth A], J [auth B], K [auth C], P [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain P [auth D]
A1IWE (Subject of Investigation/LOI) Query on A1IWE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	G [auth A], I [auth B], L [auth C], O [auth D]	1-[4-[2-[(4-bromanyl-2-methyl-phenyl)amino]ethanoyl]piperazin-1-yl]propan-1-one C₁₆ H₂₂ Br N₃ O₂ PHVHIYQQMVEZAM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	F [auth A], H [auth B], M [auth C], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth D]