KRAS-G13D-GDP in complex with Cpd38 ((E)-1-((3S)-4-(7-(6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl)-6-chloro-8-fluoro-2-(((S)-2-methylenetetrahydro-1H-pyrrolizin-7a(5H)-yl)methoxy)quinazolin-4-yl)-3-methylpiperazin-1-yl)-3-(1,2,3,4-tetrahydroisoquinolin-8-yl)prop-2-en-1-one)

Experimental Data Snapshot

  • Resolution: 1.31 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 

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Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors.

Nilewski, C.Labadie, S.Wei, B.Malhotra, S.Do, S.Gazzard, L.Liu, L.Shao, C.Murray, J.Izrayelit, Y.Gustafson, A.Endres, N.F.Ma, F.Ye, X.Zou, J.Evangelista, M.

(2024) ACS Med Chem Lett 15: 21-28

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00478
  • Primary Citation of Related Structures:  
    8UN3, 8UN4, 8UN5

  • PubMed Abstract: 

    Oncogenic KRAS mutations were identified decades ago, yet the selective inhibition of specific KRAS mutant proteins represents an ongoing challenge. Recent progress has been made in targeting certain P-loop mutant proteins, in particular KRAS G12C, for which the covalent inhibition of the GDP state via the Switch II pocket is now a clinically validated strategy. Inhibition of other KRAS mutant proteins such as KRAS G13D, on the other hand, still requires clinical validation. The remoteness of the D13 residue relative to the Switch II pocket in combination with the solvent exposure and conformational flexibility of the D13 side chain, as well as the difficulties of targeting carboxylate residues covalently, renders this specific protein particularly challenging to target selectively. In this report, we describe the design and evaluation of potent and KRAS G13D-selective reversible inhibitors. Subnanomolar binding to the GDP state Switch II pocket and biochemical selectivity over WT KRAS are achieved by leveraging a salt bridge with D13.

  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
169Homo sapiensMutation(s): 1 
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
XQ6 (Subject of Investigation/LOI)
Query on XQ6

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
C41 H43 Cl F4 N8 O2
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
C10 H15 N5 O11 P2
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.31 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.96α = 90.17
b = 41.62β = 91.35
c = 55.55γ = 116.28
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-12-20 
  • Deposition Author(s): Ultsch, M.H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references