8B6I | pdb_00008b6i

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.241 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8B6I

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Discovery of AZD4747, a Potent and Selective Inhibitor of Mutant GTPase KRAS G12C with Demonstrable CNS Penetration.

Kettle, J.G.Bagal, S.K.Barratt, D.Bodnarchuk, M.S.Boyd, S.Braybrooke, E.Breed, J.Cassar, D.J.Cosulich, S.Davies, M.Davies, N.L.Deng, C.Eatherton, A.Evans, L.Feron, L.J.Fillery, S.Gleave, E.S.Goldberg, F.W.Cortes Gonzalez, M.A.Guerot, C.Haider, A.Harlfinger, S.Howells, R.Jackson, A.Johnstrom, P.Kemmitt, P.D.Koers, A.Kondrashov, M.Lamont, G.M.Lamont, S.Lewis, H.J.Liu, L.Mylrea, M.Nash, S.Niedbala, M.J.Peter, A.Phillips, C.Pike, K.Raubo, P.Robb, G.R.Ross, S.Sanders, M.G.Schou, M.Simpson, I.Steward, O.

(2023) J Med Chem 66: 9147-9160

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00746
  • Primary Citation Related Structures: 
    8B6I, 8B78

  • PubMed Abstract: 

    The glycine to cysteine mutation at codon 12 of Kirsten rat sarcoma (KRAS) 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 14 , AZD4747, a clinical development candidate for the treatment of KRAS G12C -positive tumors, including the treatment of central nervous system (CNS) metastases. Building on our earlier discovery of C5-tethered quinazoline AZD4625, excision of a usually critical pyrimidine ring yielded a weak but brain-penetrant start point which was optimized for potency and DMPK. Key design principles and measured parameters that give high confidence in CNS exposure are discussed. During optimization, divergence between rodent and non-rodent species was observed in CNS exposure, with primate PET studies ultimately giving high confidence in the expected translation to patients. AZD4747 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: 40.54 kDa 
  • Atom Count: 3,091 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
170Homo sapiensMutation(s): 4 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
PQI
(Subject of Investigation/LOI)

Query on PQI



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
1-[(4~{a}~{S})-7-chloranyl-8-(5-methyl-2~{H}-indazol-4-yl)-1,2,4,4~{a},5,11-hexahydropyrazino[2,1-c][1,4]benzoxazepin-3-yl]propan-1-one
C23 H25 Cl N4 O2
TUSIXDDNOBGGRH-INIZCTEOSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.241 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.65α = 95.63
b = 39.19β = 95.18
c = 65.59γ = 103.25
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2023-07-26
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary