9C1R | pdb_00009c1r

Crystal structure of mutant cMET D1228N kinase domain in complex with inhibitor compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Pyrazolopyrazines as Selective, Potent, and Mutant-Active MET Inhibitors with Intracranial Efficacy.

Bumpers, Q.A.Pipal, R.W.Benz-Weeden, A.M.Brewster 2nd, J.T.Cook, A.Crooks, A.L.Cruz, C.Dwulet, N.C.Gaudino, J.J.Golec, D.Harrison, J.A.Hartley, D.P.Hassanien, S.H.Hicken, E.J.Kahn, D.Laird, E.R.Lemieux, C.Lewandowski, N.McCown, J.McDonald, M.G.McNulty, O.Mou, T.C.Nguyen, P.Oko, L.Opie, L.P.Otten, J.Peck, S.C.Polites, V.C.Randall, S.D.Rosen, R.Z.Savechenkov, P.Simpson, H.Singh, A.Sparks, D.Wickersham, K.Wollenberg, L.Wong, C.E.Wong, J.Wu, W.I.Elsayed, M.S.A.Hinklin, R.J.Tang, T.P.

(2024) J Med Chem 67: 14466-14477

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01232
  • Primary Citation Related Structures: 
    9C1R

  • PubMed Abstract: 

    Mesenchymal-epithelial transition factor (MET) is a receptor tyrosine kinase that serves a critical function in numerous developmental, morphogenic, and proliferative signaling pathways. If dysregulated, MET has been shown to be involved in the development and survival of several cancers, including non-small cell lung cancer (NSCLC), renal cancer, and other epithelial tumors. Currently, the clinical efficacy of FDA approved MET inhibitors is limited by on-target acquired resistance, dose-limiting toxicities, and less than optimal efficacy against brain metastasis. Therefore, there is still an unmet medical need for the development of MET inhibitors to address these issues. Herein we report the application of structure-based design for the discovery and development of a novel class of brain-penetrant MET inhibitors with enhanced activity against clinically relevant mutations and improved selectivity. Compound 13 with a MET D1228N cell line IC 50 value of 23 nM showed good efficacy in an intracranial tumor model and increased the median overall survival of the animals to 100% when dosed orally at 100 mg/kg daily for 21 days.


  • Organizational Affiliation
    • Pfizer Research & Development 3200 Walnut Street, Boulder, Colorado 80301, United States.

Macromolecule Content 

  • Total Structure Weight: 35.65 kDa 
  • Atom Count: 2,741 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 307 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor307Homo sapiensMutation(s): 1 
Gene Names: MET
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
PHAROS:  P08581
GTEx:  ENSG00000105976 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ATS
(Subject of Investigation/LOI)

Query on A1ATS



Download:Ideal Coordinates CCD File
C [auth A]N-(2,5-difluoro-4-{[(1s,3S)-3-(1-methyl-1H-pyrazol-3-yl)cyclobutyl][(8R)-pyrazolo[1,5-a]pyrazin-4-yl]amino}phenyl)-2-(5-fluoropyridin-2-yl)-3-oxo-2,3-dihydropyridazine-4-carboxamide
C30 H23 F3 N10 O2
JZBISQRYUUZSEV-VYOWRKJJSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.604α = 90
b = 62.248β = 90
c = 113.285γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references