3CJF

Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 3CJF

Classification: TRANSFERASE

Total Structure Weight: 36282.60

Macromolecule Entities
Molecule Chains Length Organism Details
Vascular endothelial growth factor receptor 2 A 309 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: kinase domain; residues 806-939 and 994-1168
Mutation: K833N
Gene Name(s): KDR Gene View FLK1 VEGFR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5- trimethoxyphenyl)pyrimidine-2,4-diamine
C21 H22 N6 O3
SQQAPOSROFWHIB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAV N/A in BindingDB
IC50: 6.3 nM  BindingMOAD
IC50: 6.3 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
A L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.204
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 37.44 α = 90.00
b = 94.74 β = 90.00
c = 96.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-12
  • Released Date: 2008-10-07
  • Deposition author(s): Nolte, R.T.

Revision History

  • Version 1_0: 2008-10-07

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Refinement description, Version format compliance

  • Version 1_2: 2017-08-23

    Type: Source and taxonomy