5UR9

Enantiomer-Specific Binding of the Potent Antinociceptive Agent SBFI-26 to Anandamide transporters FABP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8KSClick on this verticalbar to view detailsBest fitted MYRClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites.

Hsu, H.C.Tong, S.Zhou, Y.Elmes, M.W.Yan, S.Kaczocha, M.Deutsch, D.G.Rizzo, R.C.Ojima, I.Li, H.

(2017) Biochemistry 56: 3454-3462

  • DOI: https://doi.org/10.1021/acs.biochem.7b00194
  • Primary Citation of Related Structures:  
    5UR9, 5URA

  • PubMed Abstract: 

    Human FABP5 and FABP7 are intracellular endocannabinoid transporters. SBFI-26 is an α-truxillic acid 1-naphthyl monoester that competitively inhibits the activities of FABP5 and FABP7 and produces antinociceptive and anti-inflammatory effects in mice. The synthesis of SBFI-26 yields several stereoisomers, and it is not known how the inhibitor binds the transporters. Here we report co-crystal structures of SBFI-26 in complex with human FABP5 and FABP7 at 2.2 and 1.9 Å resolution, respectively. We found that only (S)-SBFI-26 was present in the crystal structures. The inhibitor largely mimics the fatty acid binding pattern, but it also has several unique interactions. Notably, the FABP7 complex corroborates key aspects of the ligand binding pose at the canonical site previously predicted by virtual screening. In FABP5, SBFI-26 was unexpectedly found to bind at the substrate entry portal region in addition to binding at the canonical ligand-binding pocket. Our structural and binding energy analyses indicate that both R and S forms appear to bind the transporter equally well. We suggest that the S enantiomer observed in the crystal structures may be a result of the crystallization process selectively incorporating the (S)-SBFI-26-FABP complexes into the growing lattice, or that the S enantiomer may bind to the portal site more rapidly than to the canonical site, leading to an increased local concentration of the S enantiomer for binding to the canonical site. Our work reveals two binding poses of SBFI-26 in its target transporters. This knowledge will guide the development of more potent FABP inhibitors based upon the SBFI-26 scaffold.


  • Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute , Grand Rapids, Michigan 49503, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, epidermal
A, B, C, D, E
138Homo sapiensMutation(s): 0 
Gene Names: FABP5
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8KS
Query on 8KS

Download Ideal Coordinates CCD File 
CA [auth F]
EA [auth G]
I [auth A]
IA [auth H]
N [auth B]
(1S,2S,3S,4S)-3-{[(naphthalen-1-yl)oxy]carbonyl}-2,4-diphenylcyclobutane-1-carboxylic acid
C28 H22 O4
NVOKBONTLOAJKA-CQJMVLFOSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
HA [auth G],
KA [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
U [auth C],
Y [auth D]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
DA [auth F]
FA [auth G]
GA [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
8KS BindingDB:  5UR9 Ki: min: 790, max: 900 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.99α = 61.66
b = 78.11β = 69.61
c = 78.83γ = 78.01
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8KSClick on this verticalbar to view detailsBest fitted MYRClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA035924

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-11
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.3: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description