5D4A

Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1-yl)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis

Tagami, U.Takahashi, K.Igarashi, S.Ejima, C.Yoshida, T.Takeshita, S.Miyanaga, W.Sugiki, M.Tokumasu, M.Hatanaka, T.Kashiwagi, T.Ishikawa, K.Miyano, H.Mizukoshi, T.

(2016) ACS Med Chem Lett 7: 435-439

  • DOI: 10.1021/acsmedchemlett.6b00040
  • Primary Citation of Related Structures:  
    5D4A, 5D45, 5D48, 5D47

  • PubMed Abstract: 
  • X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activ ...

    X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors.


    Organizational Affiliation

    Institute for Innovation, Ajinomoto Co., Inc. , 1-1 Suzuki-cho, Kawasaki 210-8681, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty acid-binding protein, adipocyteA152Homo sapiensMutation(s): 0 
Gene Names: FABP4
Find proteins for P15090 (Homo sapiens)
Explore P15090 
Go to UniProtKB:  P15090
NIH Common Fund Data Resources
PHAROS  P15090
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
57Q
Query on 57Q

Download CCD File 
A
3-(2-phenyl-1H-indol-1-yl)propanoic acid
C17 H15 N O2
CPWLVJORIJEUHI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
57QKi:  1400   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.161α = 90
b = 53.719β = 90
c = 74.291γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations