9IB5 | pdb_00009ib5

Structure of 18 (BI-2493) in complex with GDP-KRAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 
    0.191 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Literature

Discovery of BI-2493, a Pan-KRAS Inhibitor Showing In Vivo Efficacy.

Broker, J.Waterson, A.G.Hodges, T.R.Abbott, J.R.Arnold, A.Bottcher, J.Braun, N.Cui, J.Fuchs, J.E.Gerstberger, T.Gogg, S.Hanner, S.Herdeis, L.Howell, L.W.Mantoulidis, A.Mayer, M.Phan, J.Rocchetti, F.Sankar, K.Sarkar, D.Schaaf, O.Sensintaffar, J.L.Sun, Q.Wunberg, T.Fesik, S.W.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00576
  • Primary Citation of Related Structures:  
    9IAP, 9IAW, 9IAY, 9IB4, 9IB5

  • PubMed Abstract: 

    KRAS is one of the most highly validated cancer targets. Here we describe the design and synthesis of two reversible pan-KRAS inhibitors, BI-2865 and BI-2493. From our KRAS G12C inhibitor program, we identified BI-2865, a potent noncovalent KRAS inhibitor that showed cellular activity against a broad spectrum of KRAS alleles and selectivity against HRAS and NRAS. Spirocyclization led to the discovery of BI-2493, a highly rigid analogue exhibiting better potency, metabolic stability, and permeability. BI-2493 shows in vivo efficacy in various KRAS mutant and KRAS wild-type amplified xenograft models and represents a promising starting point for further optimization.


  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co., KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 3 
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
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VU6 (Subject of Investigation/LOI)
Query on VU6

Download Ideal Coordinates CCD File 
E [auth A](7~{S})-2'-azanyl-3-[2-[(2~{S})-2-methylpiperazin-1-yl]pyrimidin-4-yl]spiro[5,6-dihydro-4~{H}-1,2-benzoxazole-7,4'-6,7-dihydro-5~{H}-1-benzothiophene]-3'-carbonitrile
C24 H27 N7 O S
PVOYBVVIBNPTPJ-BSEYFRJRSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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: 1.01 Å
  • R-Value Free:  0.191 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.639α = 90
b = 40.784β = 90
c = 56.002γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
BUSTERrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release