KRAS-G12D in complex with BI-2865

Experimental Data Snapshot

  • Resolution: 1.09 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Pan-KRAS inhibitor disables oncogenic signalling and tumour growth.

Kim, D.Herdeis, L.Rudolph, D.Zhao, Y.Bottcher, J.Vides, A.Ayala-Santos, C.I.Pourfarjam, Y.Cuevas-Navarro, A.Xue, J.Y.Mantoulidis, A.Broker, J.Wunberg, T.Schaaf, O.Popow, J.Wolkerstorfer, B.Kropatsch, K.G.Qu, R.de Stanchina, E.Sang, B.Li, C.McConnell, D.B.Kraut, N.Lito, P.

(2023) Nature 619: 160-166

  • DOI: https://doi.org/10.1038/s41586-023-06123-3
  • Primary Citation of Related Structures:  
    8AZR, 8AZV, 8AZX, 8AZY, 8AZZ, 8B00, 8ONV

  • PubMed Abstract: 

    KRAS is one of the most commonly mutated proteins in cancer, and efforts to directly inhibit its function have been continuing for decades. The most successful of these has been the development of covalent allele-specific inhibitors that trap KRAS G12C in its inactive conformation and suppress tumour growth in patients 1-7 . Whether inactive-state selective inhibition can be used to therapeutically target non-G12C KRAS mutants remains under investigation. Here we report the discovery and characterization of a non-covalent inhibitor that binds preferentially and with high affinity to the inactive state of KRAS while sparing NRAS and HRAS. Although limited to only a few amino acids, the evolutionary divergence in the GTPase domain of RAS isoforms was sufficient to impart orthosteric and allosteric constraints for KRAS selectivity. The inhibitor blocked nucleotide exchange to prevent the activation of wild-type KRAS and a broad range of KRAS mutants, including G12A/C/D/F/V/S, G13C/D, V14I, L19F, Q22K, D33E, Q61H, K117N and A146V/T. Inhibition of downstream signalling and proliferation was restricted to cancer cells harbouring mutant KRAS, and drug treatment suppressed KRAS mutant tumour growth in mice, without having a detrimental effect on animal weight. Our study suggests that most KRAS oncoproteins cycle between an active state and an inactive state in cancer cells and are dependent on nucleotide exchange for activation. Pan-KRAS inhibitors, such as the one described here, have broad therapeutic implications and merit clinical investigation in patients with KRAS-driven cancers.

  • Organizational Affiliation

    Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 2 
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
OFU (Subject of Investigation/LOI)
Query on OFU

Download Ideal Coordinates CCD File 
H [auth A](4S)-2-azanyl-4-methyl-4-[3-[4-[(1S)-1-[(2S)-1-methylpyrrolidin-1-ium-2-yl]ethoxy]pyrimidin-2-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5H-1-benzothiophene-3-carbonitrile
C23 H28 N7 O2 S
Query on GDP

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

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.09 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.158α = 90
b = 40.545β = 90
c = 55.943γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection
  • Version 1.3: 2024-02-14
    Changes: Refinement description