4CXY

Crystal structure of human FTO in complex with acylhydrazine inhibitor 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1039/c4sc02554g
  • Primary Citation of Related Structures:  
    4CXY, 4CXW, 4CXX

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE FTOA495Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGR
Query on DGR

Download Ideal Coordinates CCD File 
B [auth A](E)-4-(2-Nicotinoylhydrazinyl)-4-oxobut-2-enoic acid
C10 H9 N3 O4
PMTJSWVYLYQGEU-ONEGZZNKSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.92α = 90
b = 141.92β = 90
c = 83.771γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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