8WE3

Crystal structure of human FABP4 complexed with C7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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Literature

Structure-based design of potent FABP4 inhibitors with high selectivity against FABP3.

Chen, G.Xie, H.You, M.Liu, J.Shao, Q.Li, M.Su, H.Xu, Y.

(2023) Eur J Med Chem 264: 115984-115984

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115984
  • Primary Citation of Related Structures:  
    8WDX, 8WE3

  • PubMed Abstract: 

    Fatty-acid binding protein 4 (FABP4) presents an attractive target for therapeutic intervention in metabolic and inflammatory diseases in recent years. However, highly similar three-dimensional structures and fatty acid binding ability of multiple FABP family members pose a significant challenge in design of FABP4-selective inhibitors. Particularly, inhibition of FABP3 raises safety concerns such as cardiac dysfunction and exercise intolerance. Here, we reported the discovery of new FABP4 inhibitors with high selectivity over FABP3 by exploiting the little structural difference in the ligand binding pockets of FABP4 and FABP3. On the basis of our previously reported FABP4 inhibitors with nanomolar potency, different substituents were further introduced to perfectly occupy two sub-pockets of FABP4 that are distinct from those of FABP3. Remarkably, a single methyl group introduction leads to the discovery of compound C3 that impressively exhibits a 601-fold selectivity over FABP3 when maintained nanomolar binding affinity for FABP4. Moreover, C3 also shows good metabolic stability and potent cellular anti-inflammatory activity, making it a promising inhibitor for further development. Therefore, the present study highlights the utility of the structure-based rational design strategy for seeking highly selective and potent inhibitors of FABP4 and the importance of identifying the appropriate subsite as well as substituent for gaining the desired selectivity.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, adipocyte152Homo sapiensMutation(s): 0 
Gene Names: FABP4
UniProt & NIH Common Fund Data Resources
Find proteins for P15090 (Homo sapiens)
Explore P15090 
Go to UniProtKB:  P15090
PHAROS:  P15090
GTEx:  ENSG00000170323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15090
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W6B (Subject of Investigation/LOI)
Query on W6B

Download Ideal Coordinates CCD File 
B [auth A]2-[(3-chloranyl-2-phenyl-phenyl)amino]-5-fluoranyl-benzoic acid
C19 H13 Cl F N O2
SQBLSUWMJNVDPR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.437α = 90
b = 54.171β = 90
c = 75.492γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release