3HK1 | pdb_00003hk1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 Related Structures: 
    3HK1

  • 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.

Macromolecule Content 

  • Total Structure Weight: 14.88 kDa 
  • Atom Count: 1,269 
  • Modeled Residue Count: 131 
  • Deposited Residue Count: 131 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, adipocyte131Mus musculusMutation(s): 0 
Gene Names: adipocyteAp2Fabp4fatty acid binding protein 4
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B64

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
GJODSFZNKNHKML-PLNGDYQASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

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