6T5U

KRasG12C ligand complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 2.0 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.

    Related Citations: 
    • KRasG12C ligand complex
      Phillips, C.
      () To be published --: --
    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
V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_bA, B168Homo sapiensMutation(s): 0 
Gene Names: KRAS, hCG_14731, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A1S2ZE25 (Erinaceus europaeus)
Explore A0A1S2ZE25 
Go to UniProtKB:  A0A1S2ZE25
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 GroupsP01116A0A1S2ZE25
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MKW (Subject of Investigation/LOI)
Query on MKW
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		1-[(7R)-16-chloro-15-(5-methyl-1H-indazol-4-yl)-9-oxa-2,5,12-triazatetracyclo[8.8.0.02,7.013,18]octadeca-1(10),11,13,15,17-pentaen-5-yl]prop-2-en-1-one
C25 H24 Cl N5 O2
FXHOZGODUVOVIF-OAHLLOKOSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.597α = 78.47
b = 41.084β = 85.59
c = 65.192γ = 68.14
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2019-10-17 
  • Released Date: 2020-02-19 
    • Deposition Author(s): Phillips, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 2.0: 2021-02-10
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary