6TAN

X-RAY STRUCTURE OF HUMAN K-RAS G12C IN COMPLEX WITH COVALENT ISOQUINOLINONE INHIBITOR (COMPOUND 17)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Computationally Empowered Workflow Identifies Novel Covalent Allosteric Binders for KRASG12C.

Mortier, J.Friberg, A.Badock, V.Moosmayer, D.Schroeder, J.Steigemann, P.Siegel, F.Gradl, S.Bauser, M.Hillig, R.C.Briem, H.Eis, K.Bader, B.Nguyen, D.Christ, C.D.

(2020) ChemMedChem 15: 827-832

  • DOI: https://doi.org/10.1002/cmdc.201900727
  • Primary Citation of Related Structures:  
    6TAM, 6TAN

  • PubMed Abstract: 

    Due to its frequent mutations in multiple lethal cancers, KRAS is one of the most-studied anticancer targets nowadays. Since the discovery of the druggable allosteric binding site containing a G12C mutation, KRAS G12C has been the focus of attention in oncology research. We report here a computationally driven approach aimed at identifying novel and selective KRAS G12C covalent inhibitors. The workflow involved initial enumeration of virtual molecules tailored for the KRAS allosteric binding site. Tools such as pharmacophore modeling, docking, and free-energy perturbations were deployed to prioritize the compounds with the best profiles. The synthesized naphthyridinone scaffold showed the ability to react with G12C and inhibit KRAS G12C . Analogues were prepared to establish structure-activity relationships, while molecular dynamics simulations and crystallization of the inhibitor-KRAS G12C complex highlighted an unprecedented binding mode.


  • Organizational Affiliation

    Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 4 
Gene Names: KRASKRAS2RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  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 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MZN (Subject of Investigation/LOI)
Query on MZN

Download Ideal Coordinates CCD File 
D [auth A]7-(2-fluoranyl-6-oxidanyl-phenyl)-3-[(3~{R})-1-propanoylpyrrolidin-3-yl]-4~{H}-2,6-naphthyridin-1-one
C21 H20 F N3 O3
RWOYGQRZJZBHOJ-GFCCVEGCSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.26α = 90
b = 58.747β = 90
c = 65.634γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-06-03
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description