9IB4 | pdb_00009ib4

Structure of 12 in complex with GDP-KRAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 
    0.239 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IB4

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 68: 15649-15668

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00576
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 20.36 kDa 
  • Atom Count: 1,625 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
A1I1Z
(Subject of Investigation/LOI)

Query on A1I1Z



Download:Ideal Coordinates CCD File
F [auth A](4~{S})-2-azanyl-4-methyl-4-[3-[2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]pyrimidin-4-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile
C22 H25 N7 O2 S
XLEYQXWFBWKQPF-XMHCIUCPSA-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],
E [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: 1.06 Å
  • R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.871α = 90
b = 40.447β = 90
c = 56γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
BUSTERrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2025-08-27
    Changes: Database references