4IE6

Crystal structure of the human fat mass and obesity associated protein (FTO) in complex with N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for inhibition of the fat mass and obesity associated protein (FTO)

Aik, W.S.Demetriades, M.Hamdan, M.K.K.Bagg, E.A.L.Yeoh, K.K.Lejeune, C.Zhang, Z.McDonough, M.A.Schofield, C.J.

(2013) J Med Chem 56: 3680-3688

  • DOI: https://doi.org/10.1021/jm400193d
  • Primary Citation of Related Structures:  
    4IDZ, 4IE0, 4IE4, 4IE5, 4IE6, 4IE7

  • PubMed Abstract: 

    The fat mass and obesity associated protein (FTO) is a potential target for anti-obesity medicines. FTO is a 2-oxoglutarate (2OG)-dependent N-methyl nucleic acid demethylase that acts on substrates including 3-methylthymidine, 3-methyluracil, and 6-methyladenine. To identify FTO inhibitors, we screened a set of 2OG analogues and related compounds using differential scanning fluorometry- and liquid chromatography-based assays. The results revealed sets of both cyclic and acyclic 2OG analogues that are FTO inhibitors. Identified inhibitors include small molecules that have been used in clinical studies for the inhibition of other 2OG oxygenases. Crystallographic analyses reveal inhibition by 2OG cosubstrate or primary substrate competitors as well as compounds that bind across both cosubstrate and primary substrate binding sites. The results will aid the development of more potent and selective FTO inhibitors.


  • Organizational Affiliation

    Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO495Homo sapiensMutation(s): 0 
Gene Names: FTOKIAA1752
EC: 1.14.11 (PDB Primary Data), 1.14.11.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens)
Explore Q9C0B1 
Go to UniProtKB:  Q9C0B1
PHAROS:  Q9C0B1
GTEx:  ENSG00000140718 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C0B1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UN9 PDBBind:  4IE6 IC50: 2800 (nM) from 1 assay(s)
BindingDB:  4IE6 IC50: 2800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.458α = 90
b = 141.458β = 90
c = 83.807γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
GDAdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2013-07-31
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description