6T5B

KRasG12C ligand complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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

    Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA170Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O7K (Subject of Investigation/LOI)
Query on O7K

Download Ideal Coordinates CCD File 
D [auth A]pyrazinoquinolinone
C25 H23 Cl F2 N4 O3
PJYYTOVRCBFDTN-SJKOYZFVSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.973α = 65.49
b = 36.569β = 74.17
c = 37.129γ = 77.61
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2019-10-15 
  • Released Date: 2020-02-26 
  • Deposition Author(s): Phillips, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references