2X9F

EPHB4 KINASE DOMAIN INHIBITOR COMPLEX

Structural Biology Knowledgebase: 2X9F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2X9F

Classification: TRANSFERASE

Total Structure Weight: 34364.13

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

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
X9F
Query on X9F

A N^4^-1H-INDAZOL-4-YL-N^2^-[3-(METHYLSULFONYL)PHENYL]PYRIMIDINE- 2,4-DIAMINE
C18 H16 N6 O2 S
FIWCLCRWDUELGO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X9F IC50: 61 - 2530 nM (99) BindingDB

IC50: 61 nM  BindingMOAD
IC50: 61 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.157
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.12 α = 90.00
b = 52.48 β = 112.05
c = 61.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-17
  • Released Date: 2010-09-29
  • Deposition author(s): Read, J., Brassington, C.A., Green, I., Mccall, E.J., Valentine, A.L., Barratt, D.

Revision History

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