Crystal structure of human KRAS G12C covalently bound with Taiho WO2020/085493A1 compound 6

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Modeling receptor flexibility in the structure-based design of KRAS G12C inhibitors.

Zhu, K.Li, C.Wu, K.Y.Mohr, C.Li, X.Lanman, B.

(2022) J Comput Aided Mol Des 36: 591-604

  • DOI: https://doi.org/10.1007/s10822-022-00467-0
  • Primary Citation of Related Structures:  
    8DNI, 8DNJ, 8DNK

  • PubMed Abstract: 

    KRAS has long been referred to as an 'undruggable' target due to its high affinity for its cognate ligands (GDP and GTP) and its lack of readily exploited allosteric binding pockets. Recent progress in the development of covalent inhibitors of KRAS G12C has revealed that occupancy of an allosteric binding site located between the α3-helix and switch-II loop of KRAS G12C -sometimes referred to as the 'switch-II pocket'-holds great potential in the design of direct inhibitors of KRAS G12C . In studying diverse switch-II pocket binders during the development of sotorasib (AMG 510), the first FDA-approved inhibitor of KRAS G12C , we found the dramatic conformational flexibility of the switch-II pocket posing significant challenges toward the structure-based design of inhibitors. Here, we present our computational approaches for dealing with receptor flexibility in the prediction of ligand binding pose and binding affinity. For binding pose prediction, we modified the covalent docking program CovDock to allow for protein conformational mobility. This new docking approach, termed as FlexCovDock, improves success rates from 55 to 89% for binding pose prediction on a dataset of 10 cross-docking cases and has been prospectively validated across diverse ligand chemotypes. For binding affinity prediction, we found standard free energy perturbation (FEP) methods could not adequately handle the significant conformational change of the switch-II loop. We developed a new computational strategy to accelerate conformational transitions through the use of targeted protein mutations. Using this methodology, the mean unsigned error (MUE) of binding affinity prediction were reduced from 1.44 to 0.89 kcal/mol on a set of 14 compounds. These approaches were of significant use in facilitating the structure-based design of KRAS G12C inhibitors and are anticipated to be of further use in the design of covalent (and noncovalent) inhibitors of other conformationally labile protein targets.

  • Organizational Affiliation

    Department of Molecular Engineering, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA. kzhu@amgen.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas184Homo sapiensMutation(s): 4 
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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U50 (Subject of Investigation/LOI)
Query on U50

Download Ideal Coordinates CCD File 
D [auth A]2-{[(5-tert-butyl-6-chloro-1H-indazol-3-yl)amino]methyl}-4-chloro-1-methyl-N-(1-propanoylazetidin-3-yl)-1H-imidazole-5-carboxamide
C23 H29 Cl2 N7 O2
Query on GDP

Download Ideal Coordinates CCD File 
C10 H15 N5 O11 P2
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.181α = 90
b = 91.181β = 90
c = 91.181γ = 90
Software Package:
Software NamePurpose
BOSdata collection
DIALSdata reduction
xia2data scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-17 
  • Deposition Author(s): Mohr, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description