9XB0 | pdb_00009xb0

Crystal structure of KRAS-G12D/Y96S mutant in complex with MRTX-1133

PDB DOI: https://doi.org/10.2210/pdb9XB0/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-23 Released: 2026-10-28
Deposition Author(s): Zhang, X.L., Zhang, X.Y., Zhang, Y.Z., Liu, L., Xu, C., Bai, F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free:
0.177 (Depositor), 0.180 (DCC)
R-Value Work:
0.153 (Depositor), 0.156 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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Literature

Crystal structure of KRAS-G12D/Y96S mutant in complex with MRTX-1133

Zhang, X.L., Zhang, X.Y., Zhang, Y.Z., Liu, L., Xu, C., Bai, F.

To be published.

Macromolecule Content

Total Structure Weight: 22.67 kDa
Atom Count: 1,598
Modeled Residue Count: 170
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A	189	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6IC (Subject of Investigation/LOI) Query on 6IC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol C₃₃ H₃₁ F₃ N₆ O₂ SCLLZBIBSFTLIN-INOGPEIASA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.177 (Depositor), 0.180 (DCC)
R-Value Work: 0.153 (Depositor), 0.156 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.491	α = 90
b = 51.726	β = 90
c = 88.114	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release