4EKG

Crystal Structure of DOT1L in Complex with EPZ003696

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Conformational adaptation drives potent, selective and durable inhibition of the human protein methyltransferase DOT1L.

Basavapathruni, A., Jin, L., Daigle, S.R., Majer, C.R., Therkelsen, C.A., Wigle, T.J., Kuntz, K.W., Chesworth, R., Pollock, R.M., Scott, M.P., Moyer, M.P., Richon, V.M., Copeland, R.A., Olhava, E.J.

(2012) Chem Biol Drug Des 80: 971-980

  • DOI: 10.1111/cbdd.12050
  • Primary Citation of Related Structures:  
    4EK9, 4EKG, 4EKI

  • PubMed Abstract: 

    • DOT1L is the human protein methyltransferase responsible for catalyzing the methylation of histone H3 on lysine 79 (H3K79). The ectopic activity of DOT1L, associated with the chromosomal translocation that is a universal hallmark of MLL-rearranged leukem ...

    DOT1L is the human protein methyltransferase responsible for catalyzing the methylation of histone H3 on lysine 79 (H3K79). The ectopic activity of DOT1L, associated with the chromosomal translocation that is a universal hallmark of MLL-rearranged leukemia, is a required driver of leukemogenesis in this malignancy. Here, we present studies on the structure-activity relationship of aminonucleoside-based DOT1L inhibitors. Within this series, we find that improvements in target enzyme affinity and selectivity are driven entirely by diminution of the dissociation rate constant for the enzyme-inhibitor complex, leading to long residence times for the binary complex. The biochemical K(i) and residence times measured for these inhibitors correlate well with their effects on intracellular H3K79 methylation and MLL-rearranged leukemic cell killing. Crystallographic studies reveal a conformational adaptation mechanism associated with high-affinity inhibitor binding and prolonged residence time; these studies also suggest that conformational adaptation likewise plays a critical role in natural ligand interactions with the enzyme, hence, facilitating enzyme turnover. These results provide critical insights into the role of conformational adaptation in the enzymatic mechanism of catalysis and in pharmacologic intervention for DOT1L and other members of this enzyme class.

    Organizational Affiliation: 

    Epizyme Inc., 325 Vassar Street, Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific A425Homo sapiensMutation(s): 0 
Gene Names: DOT1L, KIAA1814, KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
Find proteins for Q8TEK3 (Homo sapiens)
Explore Q8TEK3 
Go to UniProtKB:  Q8TEK3
NIH Common Fund Data Resources
PHAROS:  Q8TEK3
GTEx:  ENSG00000104885
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QJ
Query on 0QJ
Download Ideal Coordinates CCD File 
A
5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(methyl)amino]-5'-deoxyadenosine
C25 H36 N8 O4
DHTNDMXCZIAPMX-ZDXOVATRSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0QJKd :  1.7000000476837158   nM  PDBBind
0QJKi:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.6α = 90
b = 157.6β = 90
c = 49.15γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-04-09 
  • Released Date: 2012-10-17 
    • Deposition Author(s): Jin, L.

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references