6USX | pdb_00006usx

Identification of the Clinical Development Candidate MRTX849, a Covalent KRASG12C Inhibitor for the Treatment of Cancer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.250 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.192 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of the Clinical Development CandidateMRTX849, a Covalent KRASG12CInhibitor for the Treatment of Cancer.

Fell, J.B.Fischer, J.P.Baer, B.R.Blake, J.F.Bouhana, K.Briere, D.M.Brown, K.D.Burgess, L.E.Burns, A.C.Burkard, M.R.Chiang, H.Chicarelli, M.J.Cook, A.W.Gaudino, J.J.Hallin, J.Hanson, L.Hartley, D.P.Hicken, E.J.Hingorani, G.P.Hinklin, R.J.Mejia, M.J.Olson, P.Otten, J.N.Rhodes, S.P.Rodriguez, M.E.Savechenkov, P.Smith, D.J.Sudhakar, N.Sullivan, F.X.Tang, T.P.Vigers, G.P.Wollenberg, L.Christensen, J.G.Marx, M.A.

(2020) J Med Chem 63: 6679-6693

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02052
  • Primary Citation Related Structures: 
    6USX, 6USZ, 6UT0

  • PubMed Abstract: 

    Capping off an era marred by drug development failures and punctuated by waning interest and presumed intractability toward direct targeting of KRAS, new technologies and strategies are aiding in the target's resurgence. As previously reported, the tetrahydropyridopyrimidines were identified as irreversible covalent inhibitors of KRAS G12C that bind in the switch-II pocket of KRAS and make a covalent bond to cysteine 12. Using structure-based drug design in conjunction with a focused in vitro absorption, distribution, metabolism and excretion screening approach, analogues were synthesized to increase the potency and reduce metabolic liabilities of this series. The discovery of the clinical development candidate MRTX849 as a potent, selective covalent inhibitor of KRAS G12C is described.


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

Macromolecule Content 

  • Total Structure Weight: 40.67 kDa 
  • Atom Count: 2,894 
  • Modeled Residue Count: 336 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
170Homo 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M1R
(Subject of Investigation/LOI)

Query on M1R



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
1-{4-[2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one
C30 H38 N6 O2
PCPBPWDPZNCVFV-QHCPKHFHSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.192 (DCC) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.57α = 90
b = 156.49β = 90
c = 62.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary