7R0Q

KRasG12C in complex with GDP and compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery, Preclinical Characterization, and Early Clinical Activity of JDQ443, a Structurally Novel, Potent, and Selective Covalent Oral Inhibitor of KRASG12C.

Weiss, A.Lorthiois, E.Barys, L.Beyer, K.S.Bomio-Confaglia, C.Burks, H.Chen, X.Cui, X.de Kanter, R.Dharmarajan, L.Fedele, C.Gerspacher, M.Guthy, D.A.Head, V.Jaeger, A.Nunez, E.J.Kearns, J.D.Leblanc, C.Maira, S.M.Murphy, J.Oakman, H.Ostermann, N.Ottl, J.Rigollier, P.Roman, D.Schnell, C.Sedrani, R.Shimizu, T.Stringer, R.Vaupel, A.Voshol, H.Wessels, P.Widmer, T.Wilcken, R.Xu, K.Zecri, F.Farago, A.F.Cotesta, S.Brachmann, S.M.

(2022) Cancer Discov 12: 1500-1517

  • DOI: https://doi.org/10.1158/2159-8290.CD-22-0158
  • Primary Citation of Related Structures:  
    7R0M, 7R0N, 7R0Q

  • PubMed Abstract: 

    Covalent inhibitors of KRASG12C have shown antitumor activity against advanced/metastatic KRASG12C-mutated cancers, though resistance emerges and additional strategies are needed to improve outcomes. JDQ443 is a structurally unique covalent inhibitor of GDP-bound KRASG12C that forms novel interactions with the switch II pocket. JDQ443 potently inhibits KRASG12C-driven cellular signaling and demonstrates selective antiproliferative activity in KRASG12C-mutated cell lines, including those with G12C/H95 double mutations. In vivo, JDQ443 induces AUC exposure-driven antitumor efficacy in KRASG12C-mutated cell-derived (CDX) and patient-derived (PDX) tumor xenografts. In PDX models, single-agent JDQ443 activity is enhanced by combination with inhibitors of SHP2, MEK, or CDK4/6. Notably, the benefit of JDQ443 plus the SHP2 inhibitor TNO155 is maintained at reduced doses of either agent in CDX models, consistent with mechanistic synergy. JDQ443 is in clinical development as monotherapy and in combination with TNO155, with both strategies showing antitumor activity in patients with KRASG12C-mutated tumors.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
170Homo sapiensMutation(s): 4 
Gene Names: KRASKRAS2RASK2
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
GDP
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
H0O (Subject of Investigation/LOI)
Query on H0O

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
~{N}-[4-[3,5-dimethyl-4-(5-methyl-2~{H}-indazol-4-yl)pyrazol-1-yl]phenyl]propanamide
C22 H23 N5 O
QQALNIZCKVOIBC-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.23α = 76.89
b = 39.8β = 81.2
c = 62.81γ = 77.32
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: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description