4QKN

Crystal structure of FTO bound to a selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.3 of the entry. See complete history


Literature

Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5.

Huang, Y.Yan, J.Li, Q.Li, J.Gong, S.Zhou, H.Gan, J.Jiang, H.Jia, G.F.Luo, C.Yang, C.G.

(2015) Nucleic Acids Res 43: 373-384

  • DOI: https://doi.org/10.1093/nar/gku1276
  • Primary Citation of Related Structures:  
    4QKN

  • PubMed Abstract: 

    Two human demethylases, the fat mass and obesity-associated (FTO) enzyme and ALKBH5, oxidatively demethylate abundant N(6)-methyladenosine (m(6)A) residues in mRNA. Achieving a method for selective inhibition of FTO over ALKBH5 remains a challenge, however. Here, we have identified meclofenamic acid (MA) as a highly selective inhibitor of FTO. MA is a non-steroidal, anti-inflammatory drug that mechanistic studies indicate competes with FTO binding for the m(6)A-containing nucleic acid. The structure of FTO/MA has revealed much about the inhibitory function of FTO. Our newfound understanding, revealed herein, of the part of the nucleotide recognition lid (NRL) in FTO, for example, has helped elucidate the principles behind the selectivity of FTO over ALKBH5. Treatment of HeLa cells with the ethyl ester form of MA (MA2) has led to elevated levels of m(6)A modification in mRNA. Our collective results highlight the development of functional probes of the FTO enzyme that will (i) enable future biological studies and (ii) pave the way for the rational design of potent and specific inhibitors of FTO for use in medicine.


  • Organizational Affiliation

    CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO476Homo sapiensMutation(s): 0 
Gene Names: FTO
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens)
Explore Q9C0B1 
Go to UniProtKB:  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
OGA BindingDB:  4QKN IC50: 4.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.26α = 90
b = 141.26β = 90
c = 83.58γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection