7OO7 | pdb_00007oo7

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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: 40.38 kDa 
  • Atom Count: 2,966 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 338 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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), 0.231 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.199 (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 


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