8R7X

Kras G12D in complex with compound 4

• PDB DOI: https://doi.org/10.2210/pdb8R7X/pdb

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


• Deposited: 2023-11-27 Released: 2024-10-02 
• Deposition Author(s): Kessler, D., Zak, K.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Kras G12D in complex with compound 4

Zak, K.M., Kessler, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.13 kDa 
• Atom Count: 3,142 
• Modelled Residue Count: 334 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B	170	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	C [auth A], E [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
YFJ (Subject of Investigation/LOI)	F [auth B]	8-pyridin-4-yl-2,3,4,9-tetrahydropyrido[3,4-b]indol-1-one C16 H13 N3 O SLQNWICAFNPZCB-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.192 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.673	α = 90
b = 71.919	β = 103.41
c = 54.53	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Kessler, D., Zak, K.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release