Crystal structure of human FTO in complex with acylhydrazine inhibitor 16

Experimental Data Snapshot

  • Resolution: 2.76 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


A strategy based on nucleotide specificity leads to a subfamily-selective and cell-active inhibitor ofN6-methyladenosine demethylase FTO.

Toh, J.D.W.Sun, L.Lau, L.Z.M.Tan, J.Low, J.J.A.Tang, C.W.Q.Cheong, E.J.Y.Tan, M.J.H.Chen, Y.Hong, W.Gao, Y.G.Woon, E.C.Y.

(2015) Chem Sci 6: 112-122

  • DOI: https://doi.org/10.1039/c4sc02554g
  • Primary Citation of Related Structures:  
    4CXW, 4CXX, 4CXY

  • PubMed Abstract: 

    The AlkB family of nucleic acid demethylases are of intense biological and medical interest because of their roles in nucleic acid repair and epigenetic modification. However their functional and molecular mechanisms are unclear, hence, there is strong interest in developing selective inhibitors for them. Here we report the identification of key residues within the nucleotide-binding sites of the AlkB subfamilies that likely determine their substrate specificity. We further provide proof of principle that a strategy exploiting these inherent structural differences can enable selective and potent inhibition of the AlkB subfamilies. This is demonstrated by the first report of a subfamily-selective and cell-active FTO inhibitor 12 . The distinct selectivity of 12 for FTO against other AlkB subfamilies and 2OG oxygenases shall be of considerable interest with regards to its potential use as a functional probe. The strategy outlined here is likely applicable to other AlkB subfamilies, and, more widely, to other 2OG oxygenases.

  • Organizational Affiliation

    Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . Email: esther.woon@nus.edu.sg ; ; Tel: +65 6516 2932.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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 640

Download Ideal Coordinates CCD File 
C [auth A](2E)-4-{N'-[4-(4-tert-Butyl-benzyl)-pyridine-3-carbonyl]-hydrazino}-4-oxo-but-2-enoic acid
C21 H23 N3 O4
Query on NI

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.76 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.717α = 90
b = 140.717β = 90
c = 83.306γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Non-polymer description
  • Version 1.2: 2015-01-21
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description