3CJG

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

Structural Biology Knowledgebase: 3CJG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 3CJG

Classification: TRANSFERASE

Total Structure Weight: 36056.76

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
KIM
Query on KIM

A N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)- N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4- diamine
C22 H24 N6 O3
FLXGQDHYCWXTAI-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)
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: 2.25 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.207
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 37.70 α = 90.00
b = 95.54 β = 90.00
c = 97.01 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

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4