5YXZ | pdb_00005yxz

Co-crystal Structure of KRAS (G12C) covalently bound with Quinazoline based inhibitor JBI484

• PDB DOI: https://doi.org/10.2210/pdb5YXZ/pdb

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


• Deposited: 2017-12-07 Released: 2018-04-18 
• Deposition Author(s): Swaminathan, S., Thakur, M.K., Kandan, S., Gautam, A., Kanavalli, M., Simhadri, P., Gosu, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.237 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Co-crystal Structure of KRAS (G12C) covalently bound with Quinazoline based inhibitor JBI484

Swaminathan, S., Thakur, M.K., Kandan, S., Gautam, A., Kanavalli, M., Simhadri, P., Gosu, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.3 kDa 
• Atom Count: 1,583 
• Modeled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	170	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
94C	D [auth A]	1-[4-[6-chloranyl-8-fluoranyl-7-(2-fluorophenyl)quinazolin-4-yl]piperazin-1-yl]propan-1-one C21 H19 Cl F2 N4 O YGUHAAHXXMAGAS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.237 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.604	α = 90
b = 53.089	β = 90
c = 69.106	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Swaminathan, S., Thakur, M.K., Kandan, S., Gautam, A., Kanavalli, M., Simhadri, P., Gosu, R.

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-10-30
  Changes: Structure summary