4ER6

Crystal structure of human DOT1L in complex with inhibitor SGC0946


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.216 

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
413Homo 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 3 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
AW2
Query on AW2

Download SDF File 
Download CCD File 
A
5-bromo-7-{5-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5-deoxy-beta-D-ribofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C28 H40 Br N7 O4
IQCKJUKAQJINMK-HUBRGWSESA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AW2Kd: 0.1 nM (100) BINDINGDB
AW2EC50: 9 nM (100) BINDINGDB
AW2IC50: 0.3 - 8.8 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.216 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 149.907α = 90.00
b = 149.907β = 90.00
c = 52.839γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
31IDdata collection
PDB_EXTRACTdata extraction
MOSFLMdata reduction

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