7U8H

Discovery of a KRAS G12V Inhibitor in vivo Tool Compound starting from an HSQC-NMR based Fragment Hit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS G12C Inhibitor.

Broker, J.Waterson, A.G.Smethurst, C.Kessler, D.Bottcher, J.Mayer, M.Gmaschitz, G.Phan, J.Little, A.Abbott, J.R.Sun, Q.Gmachl, M.Rudolph, D.Arnhof, H.Rumpel, K.Savarese, F.Gerstberger, T.Mischerikow, N.Treu, M.Herdeis, L.Wunberg, T.Gollner, A.Weinstabl, H.Mantoulidis, A.Kramer, O.McConnell, D.B.W Fesik, S.

(2022) J Med Chem 65: 14614-14629

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01120
  • Primary Citation of Related Structures:  
    7U8H, 8AFB, 8AFC, 8AFD

  • PubMed Abstract: 

    Activating mutations in KRAS are the most frequent oncogenic alterations in cancer. The oncogenic hotspot position 12, located at the lip of the switch II pocket, offers a covalent attachment point for KRAS G12C inhibitors. To date, KRAS G12C inhibitors have been discovered by first covalently binding to the cysteine at position 12 and then optimizing pocket binding. We report on the discovery of the in vivo active KRAS G12C inhibitor BI-0474 using a different approach, in which small molecules that bind reversibly to the switch II pocket were identified and then optimized for non-covalent binding using structure-based design. Finally, the Michael acceptor containing warhead was attached. Our approach offers not only an alternative approach to discovering KRAS G12C inhibitors but also provides a starting point for the discovery of inhibitors against other oncogenic KRAS mutants.


  • 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 KRas
A, B, C, D
170Homo sapiensMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
Q [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
LX6 (Subject of Investigation/LOI)
Query on LX6

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
2-amino-4,5,6,7-tetrahydro-1-benzothiophene-3-carbonitrile
C9 H10 N2 S
ADHVMGAFAKSNOM-UHFFFAOYSA-N
2XO
Query on 2XO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
P [auth D]
1H-benzimidazol-2-ylmethanethiol
C8 H8 N2 S
XGIDEUICZZXBFQ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.835α = 90
b = 98.48β = 90
c = 149.888γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-01-04
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description