3OE9

Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule antagonist IT1t in P1 spacegroup

Structural Biology Knowledgebase: 3OE9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.252

Literature

Macromolecules
Sequence Display for 3OE9

Classification: SIGNALING PROTEIN HYDROLASE

Total Structure Weight: 114185.52

Macromolecule Entities
Molecule Chains Length Organism Details
C-X-C chemokine receptor type 4, Lysozyme Chimera A, B 499 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319
Mutation: L125W, C1054T, C1097A, T240P
Gene Name(s): CXCR4 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: CXCR4 chemokine receptor complexed with IT1t antagonist


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

A, B (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol- 3-yl)methyl N,N'-dicyclohexylimidothiocarbamate
C21 H34 N4 S2
OOSUDWRRWZVFEB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ITD IC50: 1.1 - 11 nM (85 - 91) BindingDB

N/A in BindingMoad
Ki: 6.6 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.252
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 72.50 α = 64.66
b = 72.74 β = 73.93
c = 84.27 γ = 61.31

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-12
  • Released Date: 2010-10-27
  • Deposition author(s): Wu, B., Mol, C.D., Han, G.W., Katritch, V., Chien, E.Y.T., Liu, W., Cherezov, V., Stevens, R.C., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D), GPCR Network (GPCR)

Revision History

  • 2012-05-02
    Type: Entry authorship | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4