4AZM | pdb_00004azm

Human epidermal fatty acid-binding protein (FABP5) in complex with the inhibitor BMS-309413


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.252 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter.

Sanson, B.Wang, T.Sun, J.Wang, L.Kaczocha, M.Ojima, I.Deutsch, D.Li, H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 290

  • DOI: https://doi.org/10.1107/S1399004713026795
  • Primary Citation Related Structures: 
    4AZM, 4AZN, 4AZO, 4AZP, 4AZQ, 4AZR

  • PubMed Abstract: 

    In addition to binding intracellular fatty acids, fatty-acid-binding proteins (FABPs) have recently been reported to also transport the endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), arachidonic acid derivatives that function as neurotransmitters and mediate a diverse set of physiological and psychological processes. To understand how the endocannabinoids bind to FABPs, the crystal structures of FABP5 in complex with AEA, 2-AG and the inhibitor BMS-309403 were determined. These ligands are shown to interact primarily with the substrate-binding pocket via hydrophobic interactions as well as a common hydrogen bond to the Tyr131 residue. This work advances our understanding of FABP5-endocannabinoid interactions and may be useful for future efforts in the development of small-molecule inhibitors to raise endocannabinoid levels.


  • Organizational Affiliation
    • Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.

Macromolecule Content 

  • Total Structure Weight: 31.98 kDa 
  • Atom Count: 2,223 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FATTY ACID-BINDING PROTEIN, EPIDERMAL
A, B
138Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01469 (Homo sapiens)
Explore Q01469 
Go to UniProtKB:  Q01469
PHAROS:  Q01469
GTEx:  ENSG00000164687 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01469
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.252 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.67α = 90
b = 104.67β = 90
c = 58.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2014-02-26
    Changes: Database references
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description