4UAI

Crystal structure of CXCL12 in complex with inhibitor

  • Classification: CYTOKINE/CYTOKINE INHIBITOR
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • 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 (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1021/jm501194p
  • Primary Citation of Related Structures:  
    4UAI

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stromal cell-derived factor 1
A, B
68Homo sapiensMutation(s): 0 
Gene Names: CXCL12, SDF1, SDF1A, SDF1B
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens)
Explore P48061 
Go to UniProtKB:  P48061
PHAROS:  P48061
GTEx:  ENSG00000107562 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48061
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.93α = 90
b = 57.71β = 90
c = 72.53γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097381
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI058072
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA173056

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 2.0: 2017-09-27
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description