6T5U

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant GTPase KRASG12C.

Kettle, J.G.Bagal, S.K.Bickerton, S.Bodnarchuk, M.S.Breed, J.Carbajo, R.J.Cassar, D.J.Chakraborty, A.Cosulich, S.Cumming, I.Davies, M.Eatherton, A.Evans, L.Feron, L.Fillery, S.Gleave, E.S.Goldberg, F.W.Harlfinger, S.Hanson, L.Howard, M.Howells, R.Jackson, A.Kemmitt, P.Kingston, J.K.Lamont, S.Lewis, H.J.Li, S.Liu, L.Ogg, D.Phillips, C.Polanski, R.Robb, G.Robinson, D.Ross, S.Smith, J.M.Tonge, M.Whiteley, R.Yang, J.Zhang, L.Zhao, X.

(2020) J Med Chem 63: 4468-4483

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01720
  • Primary Citation of Related Structures:  
    6T5B, 6T5U, 6T5V

  • PubMed Abstract: 

    Attempts to directly drug the important oncogene KRAS have met with limited success despite numerous efforts across industry and academia. The KRAS G12C mutant represents an "Achilles heel" and has recently yielded to covalent targeting with small molecules that bind the mutant cysteine and create an allosteric pocket on GDP-bound RAS, locking it in an inactive state. A weak inhibitor at this site was optimized through conformational locking of a piperazine-quinazoline motif and linker modification. Subsequent introduction of a key methyl group to the piperazine resulted in enhancements in potency, permeability, clearance, and reactivity, leading to identification of a potent KRAS G12C inhibitor with high selectivity and excellent cross-species pharmacokinetic parameters and in vivo efficacy.


  • Organizational Affiliation

    Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
A, B
168Homo sapiensMutation(s): 0 
Gene Names: KRAShCG_14731
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A1S2ZE25 (Erinaceus europaeus)
Explore A0A1S2ZE25 
Go to UniProtKB:  A0A1S2ZE25
Find proteins for P01116 (Homo sapiens)
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S2ZE25
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MKW (Subject of Investigation/LOI)
Query on MKW

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
1-[(7R)-16-chloro-15-(5-methyl-1H-indazol-4-yl)-9-oxa-2,5,12-triazatetracyclo[8.8.0.02,7.013,18]octadeca-1(10),11,13,15,17-pentaen-5-yl]prop-2-en-1-one
C25 H24 Cl N5 O2
FXHOZGODUVOVIF-OAHLLOKOSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.597α = 78.47
b = 41.084β = 85.59
c = 65.192γ = 68.14
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-02-19 
  • Deposition Author(s): Phillips, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 2.0: 2021-02-10
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description