3UWP

Crystal structure of Dot1l in complex with 5-iodotubercidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors.

Yu, W.Chory, E.J.Wernimont, A.K.Tempel, W.Scopton, A.Federation, A.Marineau, J.J.Qi, J.Barsyte-Lovejoy, D.Yi, J.Marcellus, R.Iacob, R.E.Engen, J.R.Griffin, C.Aman, A.Wienholds, E.Li, F.Pineda, J.Estiu, G.Shatseva, T.Hajian, T.Al-Awar, R.Dick, J.E.Vedadi, M.Brown, P.J.Arrowsmith, C.H.Bradner, J.E.Schapira, M.

(2012) Nat Commun 3: 1288-1288

  • DOI: 10.1038/ncomms2304
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective inhibition of protein methyltransferases is a promising new approach to drug discovery. An attractive strategy towards this goal is the development of compounds that selectively inhibit binding of the cofactor, S-adenosylmethionine, within ...

    Selective inhibition of protein methyltransferases is a promising new approach to drug discovery. An attractive strategy towards this goal is the development of compounds that selectively inhibit binding of the cofactor, S-adenosylmethionine, within specific protein methyltransferases. Here we report the three-dimensional structure of the protein methyltransferase DOT1L bound to EPZ004777, the first S-adenosylmethionine-competitive inhibitor of a protein methyltransferase with in vivo efficacy. This structure and those of four new analogues reveal remodelling of the catalytic site. EPZ004777 and a brominated analogue, SGC0946, inhibit DOT1L in vitro and selectively kill mixed lineage leukaemia cells, in which DOT1L is aberrantly localized via interaction with an oncogenic MLL fusion protein. These data provide important new insight into mechanisms of cell-active S-adenosylmethionine-competitive protein methyltransferase inhibitors, and establish a foundation for the further development of drug-like inhibitors of DOT1L for cancer therapy.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A
438Homo sapiensMutation(s): 0 
Gene Names: DOT1L (KIAA1814, KMT4)
EC: 2.1.1.43
Find proteins for Q8TEK3 (Homo sapiens)
Go to Gene View: DOT1L
Go to UniProtKB:  Q8TEK3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
5ID
Query on 5ID

Download SDF File 
Download CCD File 
A
(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
5-IODOTUBERCIDIN
C11 H13 I N4 O4
WHSIXKUPQCKWBY-IOSLPCCCSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5IDIC50: 18000 - 18200 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 149.784α = 90.00
b = 149.784β = 90.00
c = 53.521γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references