Identification and Characterization of a Small Molecule Inhibitor of Fatty Acid Binding Proteins

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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Identification and characterization of a small molecule inhibitor of Fatty Acid binding proteins.

Hertzel, A.V.Hellberg, K.Reynolds, J.M.Kruse, A.C.Juhlmann, B.E.Smith, A.J.Sanders, M.A.Ohlendorf, D.H.Suttles, J.Bernlohr, D.A.

(2009) J Med Chem 52: 6024-6031

  • DOI: https://doi.org/10.1021/jm900720m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Molecular disruption of the lipid carrier AFABP/aP2 in mice results in improved insulin sensitivity and protection from atherosclerosis. Because small molecule inhibitors may be efficacious in defining the mechanism(s) of AFABP/aP2 action, a chemical library was screened and identified 1 (HTS01037) as a pharmacologic ligand capable of displacing the fluorophore 1-anilinonaphthalene 8-sulfonic acid from the lipid binding cavity. The X-ray crystal structure of 1 bound to AFABP/aP2 revealed that the ligand binds at a structurally similar position to a long-chain fatty acid. Similar to AFABP/aP2 knockout mice, 1 inhibits lipolysis in 3T3-L1 adipocytes and reduces LPS-stimulated inflammation in cultured macrophages. 1 acts as an antagonist of the protein-protein interaction between AFABP/aP2 and hormone sensitive lipase but does not activate PPARgamma in macrophage or CV-1 cells. These results identify 1 as an inhibitor of fatty acid binding and a competitive antagonist of protein-protein interactions mediated by AFABP/aP2.

  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, adipocyte131Mus musculusMutation(s): 0 
Gene Names: adipocyteAp2Fabp4fatty acid binding protein 4
Find proteins for P04117 (Mus musculus)
Explore P04117 
Go to UniProtKB:  P04117
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04117
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B64

Download Ideal Coordinates CCD File 
B [auth A]4-{[2-(methoxycarbonyl)-5-(2-thienyl)-3-thienyl]amino}-4-oxo-2-butenoic acid
C14 H11 N O5 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
B64 Binding MOAD:  3HK1 Ki: 670 (nM) from 1 assay(s)
PDBBind:  3HK1 Ki: 670 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.017α = 90
b = 94.113β = 90
c = 49.662γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description