4UAI

Crystal structure of CXCL12 in complex with inhibitor

  • Classification: CYTOKINE/CYTOKINE INHIBITOR
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2014-08-09 Released: 2014-11-12 
  • Deposition Author(s): Smith, E.W., Chen, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Cancer Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural Analysis of a Novel Small Molecule Ligand Bound to the CXCL12 Chemokine.

Smith, E.W.Liu, Y.Getschman, A.E.Peterson, F.C.Ziarek, J.J.Li, R.Volkman, B.F.Chen, Y.

(2014) J.Med.Chem. 57: 9693-9699

  • DOI: 10.1021/jm501194p

  • PubMed Abstract: 
  • CXCL12 binds to CXCR4, promoting both chemotaxis of lymphocytes and metastasis of cancer cells. We previously identified small molecule ligands that bind CXCL12 and block CXCR4-mediated chemotaxis. We now report a 1.9 Å resolution X-ray structure of ...

    CXCL12 binds to CXCR4, promoting both chemotaxis of lymphocytes and metastasis of cancer cells. We previously identified small molecule ligands that bind CXCL12 and block CXCR4-mediated chemotaxis. We now report a 1.9 Å resolution X-ray structure of CXCL12 bound by such a molecule at a site normally bound by sY21 of CXCR4. The complex structure reveals binding hot spots for future inhibitor design and suggests a new approach to targeting CXCL12-CXCR4 signaling in drug discovery.


    Organizational Affiliation

    Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stromal cell-derived factor 1
A, B
68Homo sapiensMutation(s): 0 
Gene Names: CXCL12 (SDF1, SDF1A, SDF1B)
Find proteins for P48061 (Homo sapiens)
Go to Gene View: CXCL12
Go to UniProtKB:  P48061
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3GG
Query on 3GG

Download SDF File 
Download CCD File 
A
1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea
C14 H12 N6 O
KTIWLNFSBOCUHG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.930α = 90.00
b = 57.710β = 90.00
c = 72.530γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-08-09 
  • Released Date: 2014-11-12 
  • Deposition Author(s): Smith, E.W., Chen, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM097381
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI058072
National Institutes of Health/National Cancer InstituteUnited StatesCA173056

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 2.0: 2017-09-27
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary