7O83 | pdb_00007o83

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.291 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7O83

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of AZD4625, a Covalent Allosteric Inhibitor of the Mutant GTPase KRAS G12C .

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

(2022) J Med Chem 65: 6940-6952

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00369
  • Primary Citation Related Structures: 
    7O70, 7O83, 7OO7

  • PubMed Abstract: 

    KRAS is an archetypal high-value intractable oncology drug target. The glycine to cysteine mutation at codon 12 represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 21 , AZD4625, a clinical development candidate for the treatment of KRAS G12C positive tumors. Highlights include a quinazoline tethering strategy to lock out a bio-relevant binding conformation and an optimization strategy focused on the reduction of extrahepatic clearance mechanisms seen in preclinical species. Crystallographic analysis was also key in helping to rationalize unusual structure-activity relationship in terms of ring size and enantio-preference. AZD4625 is a highly potent and selective inhibitor of KRAS G12C with an anticipated low clearance and high oral bioavailability profile in humans.


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

Macromolecule Content 

  • Total Structure Weight: 40.09 kDa 
  • Atom Count: 2,901 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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): 4 
Gene Names: KRAShCG_14731

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V52
(Subject of Investigation/LOI)

Query on V52



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
1-[(7S)-11-chloro-12-(5-methyl-1H-indazol-4-yl)-9-oxa-2,5,15,17-tetrazatetracyclo[8.7.1.02,7.014,18]octadeca-1(17),10,12,14(18),15-pentaen-5-yl]prop-2-en-1-one
C24 H23 Cl N6 O2
PWTZCWDPTMAUQB-AWEZNQCLSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.509α = 96.39
b = 39.227β = 95.01
c = 65.721γ = 103.15
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary