3EFJ

Structure of c-Met with pyrimidone inhibitor 7

Structural Biology Knowledgebase: 3EFJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.244

Literature

Macromolecules
Sequence Display for 3EFJ

Classification: Transferase

Total Structure Weight: 71689.45

Macromolecule Entities
Molecule Chains Length Organism Details
Hepatocyte growth factor receptor A, B 310 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: c-Met kinase domain, UNP residues 1048-1351
Mutation: V1272L
Gene Name(s): MET Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MT3
Query on MT3

A, B 2-benzyl-5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]- 3-fluorophenyl}-3-methylpyrimidin-4(3H)-one
C29 H24 F N3 O4
IKPJWGNTDNCFPS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MT3 IC50: 39 nM (99) BindingDB
Ki: 39 nM (99) BindingDB

N/A in BindingMoad
Ki: 39 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.244
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.74 α = 90.00
b = 78.65 β = 90.00
c = 129.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-09
  • Released Date: 2008-10-07
  • Deposition author(s): D'Angelo, N., Bellon, S., Whittington, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4