2VX1

EPHB4 KINASE DOMAIN INHIBITOR COMPLEX

Structural Biology Knowledgebase: 2VX1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 2VX1

Classification: TRANSFERASE

Total Structure Weight: 34391.77

Macromolecule Entities
Molecule Chains Length Organism Details
EPHRIN TYPE-B RECEPTOR 4 A 302 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: KINASE DOMAIN, RESIDUES 598-899
Mutation: Y774E
Gene Name(s): EPHB4 Gene View HTK MYK1 TYRO11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
7X8
Query on 7X8

A 3-({4-[(5-CHLORO-1,3-BENZODIOXOL-4-YL)AMINO]PYRIMIDIN- 2-YL}AMINO)BENZAMIDE
C18 H14 Cl N5 O3
ZVQZIVCQLFGXFZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
7X8 IC50: 220 - 900 nM (99) BindingDB

IC50: 220 nM  BindingMOAD
IC50: 220 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.171
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.12 α = 90.00
b = 53.54 β = 110.90
c = 61.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-30
  • Released Date: 2008-10-28
  • Deposition author(s): Read, J., Brassington, C.A., Green, I., Mccall, E.J., Valentine, A.L., Barratt, D., Leach, A.G., Kettle, J.G.

Revision History

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