7OO7 | pdb_00007oo7

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VLEClick on this verticalbar to view details

This is version 1.4 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRasA,
B [auth D]
169Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VLE (Subject of Investigation/LOI)
Query on VLE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth D]
1-[(6aS)-3-chloro-2-(5-methyl-1H-indazol-4-yl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':5,6][1,5]oxazocino[4,3,2-de]quinazolin-8-yl]-2-propen-1-one
C25 H25 Cl N6 O2
NEZLXNUXFYWZNP-HNNXBMFYSA-N
GDP
Query on GDP

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

Download Ideal Coordinates CCD File 
I [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.289α = 90
b = 72.012β = 90.32
c = 65.821γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VLEClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2022-04-20 
  • Deposition Author(s): Phillips, C.

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: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary