3OE6

Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 3OE6

Classification: SIGNALING PROTEIN HYDROLASE

Total Structure Weight: 59105.79

Macromolecule Entities
Molecule Chains Length Organism Details
C-X-C chemokine receptor type 4, Lysozyme Chimera A 508 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-325
Mutation: L125W, C1054T, C1097A
Gene Name(s): E CXCR4 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ITD
Query on ITD

A (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)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ITD IC50: 11 nM (88) BindingDB

N/A in BindingMoad
Ki: 8.2 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.232
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 71.12 α = 90.00
b = 78.71 β = 90.00
c = 240.59 γ = 90.00

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

  • 2011-07-13
    Type: Version format compliance
  • 2012-05-02
    Type: Structure summary