6N2J

Tetrahydropyridopyrimidines as Covalent Inhibitors of KRAS-G12C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Tetrahydropyridopyrimidines as Irreversible Covalent Inhibitors of KRAS-G12C with In Vivo Activity.

Fell, J.B.Fischer, J.P.Baer, B.R.Ballard, J.Blake, J.F.Bouhana, K.Brandhuber, B.J.Briere, D.M.Burgess, L.E.Burkard, M.R.Chiang, H.Chicarelli, M.J.Davidson, K.Gaudino, J.J.Hallin, J.Hanson, L.Hee, K.Hicken, E.J.Hinklin, R.J.Marx, M.A.Mejia, M.J.Olson, P.Savechenkov, P.Sudhakar, N.Tang, T.P.Vigers, G.P.Zecca, H.Christensen, J.G.

(2018) ACS Med Chem Lett 9: 1230-1234

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00382
  • Primary Citation of Related Structures:  
    6N2J, 6N2K

  • PubMed Abstract: 

    KRAS is the most frequently mutated driver oncogene in human cancer, and KRAS mutations are commonly associated with poor prognosis and resistance to standard treatment. The ability to effectively target and block the function of mutated KRAS has remained elusive despite decades of research. Recent findings have demonstrated that directly targeting KRAS-G12C with electrophilic small molecules that covalently modify the mutated codon 12 cysteine is feasible. We have discovered a series of tetrahydropyridopyrimidines as irreversible covalent inhibitors of KRAS-G12C with in vivo activity. The PK/PD and efficacy of compound 13 will be highlighted.


  • Organizational Affiliation

    Array BioPharma, Inc., 3200 Walnut Street, Boulder, Colorado 80301, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo 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 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
K9M (Subject of Investigation/LOI)
Query on K9M

Download Ideal Coordinates CCD File 
D [auth A]1-{4-[7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one
C24 H27 N5 O
XUTSLHHFLGGLJU-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: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.25α = 90
b = 51.13β = 90
c = 90.12γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-12-12 
  • Deposition Author(s): Vigers, G.P.

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description