4EKG

Crystal Structure of DOT1L in Complex with EPZ003696


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 

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:  

  • 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 le ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A
425Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QJ
Query on 0QJ

Download SDF File 
Download 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 %)
0QJKi: 13 nM (100) BINDINGDB
0QJKd: 1.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 157.600α = 90.00
b = 157.600β = 90.00
c = 49.150γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
HKL-2000data collection
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references