4ER7

Crystal Structure of human DOT1L in complex with inhibitor SGC0947


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A
421Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AW3
Query on AW3

Download SDF File 
Download CCD File 
A
5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C25 H34 Br N7 O4
RFVBTQBCRYTKHX-ZDXOVATRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 150.617α = 90.00
b = 150.617β = 90.00
c = 52.800γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
31IDdata collection
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references