6OIM

Crystal Structure of human KRAS G12C covalently bound to AMG 510


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity.

Canon, J.Rex, K.Saiki, A.Y.Mohr, C.Cooke, K.Bagal, D.Gaida, K.Holt, T.Knutson, C.G.Koppada, N.Lanman, B.A.Werner, J.Rapaport, A.S.San Miguel, T.Ortiz, R.Osgood, T.Sun, J.R.Zhu, X.McCarter, J.D.Volak, L.P.Houk, B.E.Fakih, M.G.O'Neil, B.H.Price, T.J.Falchook, G.S.Desai, J.Kuo, J.Govindan, R.Hong, D.S.Ouyang, W.Henary, H.Arvedson, T.Cee, V.J.Lipford, J.R.

(2019) Nature 575: 217-223

  • DOI: 10.1038/s41586-019-1694-1
  • Primary Citation of Related Structures:  
    6OIM

  • PubMed Abstract: 
  • KRAS is the most frequently mutated oncogene in cancer and encodes a key signalling protein in tumours 1,2 . The KRAS(G12C) mutant has a cysteine residue that has been exploited to design covalent inhibitors that have promising preclinical activity 3-5 ...

    KRAS is the most frequently mutated oncogene in cancer and encodes a key signalling protein in tumours 1,2 . The KRAS(G12C) mutant has a cysteine residue that has been exploited to design covalent inhibitors that have promising preclinical activity 3-5 . Here we optimized a series of inhibitors, using novel binding interactions to markedly enhance their potency and selectivity. Our efforts have led to the discovery of AMG 510, which is, to our knowledge, the first KRAS(G12C) inhibitor in clinical development. In preclinical analyses, treatment with AMG 510 led to the regression of KRAS G12C tumours and improved the anti-tumour efficacy of chemotherapy and targeted agents. In immune-competent mice, treatment with AMG 510 resulted in a pro-inflammatory tumour microenvironment and produced durable cures alone as well as in combination with immune-checkpoint inhibitors. Cured mice rejected the growth of isogenic KRAS G12D tumours, which suggests adaptive immunity against shared antigens. Furthermore, in clinical trials, AMG 510 demonstrated anti-tumour activity in the first dosing cohorts and represents a potentially transformative therapy for patients for whom effective treatments are lacking.


    Organizational Affiliation

    Amgen Research, Amgen Inc, Thousand Oaks, CA, USA. jlipford@amgen.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA183Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOV (Subject of Investigation/LOI)
Query on MOV

Download Ideal Coordinates CCD File 
D [auth A]AMG 510 (bound form)
C30 H32 F2 N6 O3
ZIXPBHVQXGLHAG-SFHVURJKSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 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: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.868α = 90
b = 58.417β = 90
c = 65.884γ = 90
Software Package:
Software NamePurpose
BOSdata collection
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-04-09 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Mohr, C.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Derived calculations, Structure summary