Crystal structure of human FTO in complex with small-molecule inhibitors

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1.

Peng, S.Xiao, W.Ju, D.Sun, B.Hou, N.Liu, Q.Wang, Y.Zhao, H.Gao, C.Zhang, S.Cao, R.Li, P.Huang, H.Ma, Y.Wang, Y.Lai, W.Ma, Z.Zhang, W.Huang, S.Wang, H.Zhang, Z.Zhao, L.Cai, T.Zhao, Y.L.Wang, F.Nie, Y.Zhi, G.Yang, Y.G.Zhang, E.E.Huang, N.

(2019) Sci Transl Med 11

  • DOI: https://doi.org/10.1126/scitranslmed.aau7116
  • Primary Citation of Related Structures:  
    6AEJ, 6AK4

  • PubMed Abstract: 

    Recent studies have established the involvement of the fat mass and obesity-associated gene ( FTO ) in metabolic disorders such as obesity and diabetes. However, the precise molecular mechanism by which FTO regulates metabolism remains unknown. Here, we used a structure-based virtual screening of U.S. Food and Drug Administration-approved drugs to identify entacapone as a potential FTO inhibitor. Using structural and biochemical studies, we showed that entacapone directly bound to FTO and inhibited FTO activity in vitro. Furthermore, entacapone administration reduced body weight and lowered fasting blood glucose concentrations in diet-induced obese mice. We identified the transcription factor forkhead box protein O1 ( FOXO1 ) mRNA as a direct substrate of FTO, and demonstrated that entacapone elicited its effects on gluconeogenesis in the liver and thermogenesis in adipose tissues in mice by acting on an FTO-FOXO1 regulatory axis.

  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO,Alpha-ketoglutarate-dependent dioxygenase FTO470Homo sapiensMutation(s): 0 
Gene Names: FTOKIAA1752
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7YC

Download Ideal Coordinates CCD File 
B [auth A](E)-3-[3-nitro-4,5-bis(oxidanyl)phenyl]-2-(1,3-oxazinan-3-ylcarbonyl)prop-2-enenitrile
C14 H13 N3 O6
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.221 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.057α = 90
b = 142.057β = 90
c = 84.672γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALEPACKdata 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: 2019-06-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description