8AQ5

KRAS G12C IN COMPLEX WITH GDP AND COMPOUND 16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

JDQ443, a Structurally Novel, Pyrazole-Based, Covalent Inhibitor of KRAS G12C for the Treatment of Solid Tumors.

Lorthiois, E.Gerspacher, M.Beyer, K.S.Vaupel, A.Leblanc, C.Stringer, R.Weiss, A.Wilcken, R.Guthy, D.A.Lingel, A.Bomio-Confaglia, C.Machauer, R.Rigollier, P.Ottl, J.Arz, D.Bernet, P.Desjonqueres, G.Dussauge, S.Kazic-Legueux, M.Lozac'h, M.A.Mura, C.Sorge, M.Todorov, M.Warin, N.Zink, F.Voshol, H.Zecri, F.J.Sedrani, R.C.Ostermann, N.Brachmann, S.M.Cotesta, S.

(2022) J Med Chem 65: 16173-16203

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01438
  • Primary Citation of Related Structures:  
    8AQ5, 8AQ7

  • PubMed Abstract: 

    Rapid emergence of tumor resistance via RAS pathway reactivation has been reported from clinical studies of covalent KRAS G12C inhibitors. Thus, inhibitors with broad potential for combination treatment and distinct binding modes to overcome resistance mutations may prove beneficial. JDQ443 is an investigational covalent KRAS G12C inhibitor derived from structure-based drug design followed by extensive optimization of two dissimilar prototypes. JDQ443 is a stable atropisomer containing a unique 5-methylpyrazole core and a spiro-azetidine linker designed to position the electrophilic acrylamide for optimal engagement with KRAS G12C C12. A substituted indazole at pyrazole position 3 results in novel interactions with the binding pocket that do not involve residue H95. JDQ443 showed PK/PD activity in vivo and dose-dependent antitumor activity in mouse xenograft models. JDQ443 is now in clinical development, with encouraging early phase data reported from an ongoing Phase Ib/II clinical trial (NCT04699188).


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, BaselCH-4056, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 4 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NZ6 (Subject of Investigation/LOI)
Query on NZ6

Download Ideal Coordinates CCD File 
C [auth A]1-[6-[4-(5-chloranyl-6-methyl-1~{H}-indazol-4-yl)-5-methyl-3-phenyl-pyrazol-1-yl]-2-azaspiro[3.3]heptan-2-yl]propan-1-one
C27 H28 Cl N5 O
YRRYLCZNICDPLK-UHFFFAOYSA-N
GDP
Query on GDP

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

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.105α = 90
b = 40.324β = 100.95
c = 52.292γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary