3ODU

The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 3ODU

Classification: SIGNALING PROTEIN HYDROLASE

Total Structure Weight: 118216.37

Macromolecule Entities
Molecule Chains Length Organism Details
C-X-C chemokine receptor type 4, Lysozyme Chimera A, B 502 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319
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: mpstruc | 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, 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)
OLC
Query on OLC

A, B (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)
OLA
Query on OLA

A, B OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ITD IC50: 11 nM (87) BindingDB

N/A in BindingMoad
Ki: 7.3 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.237
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 64.54 α = 90.00
b = 83.69 β = 102.17
c = 120.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-11
  • 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

  • Version 1_0: 2010-10-27

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2012-05-02

    Type: Structure summary

  • Version 1_3: 2017-07-26

    Type: Refinement description, Source and taxonomy