4HRA

Crystal Structure of DOT1L in Complex with EPZ-5676


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent inhibition of DOT1L as treatment of MLL-fusion leukemia.

Daigle, S.R.Olhava, E.J.Therkelsen, C.A.Basavapathruni, A.Jin, L.Boriack-Sjodin, P.A.Allain, C.J.Klaus, C.R.Raimondi, A.Scott, M.P.Waters, N.J.Chesworth, R.Moyer, M.P.Copeland, R.A.Richon, V.M.Pollock, R.M.

(2013) Blood 122: 1017-1025

  • DOI: 10.1182/blood-2013-04-497644

  • PubMed Abstract: 
  • Rearrangements of the MLL gene define a genetically distinct subset of acute leukemias with poor prognosis. Current treatment options are of limited effectiveness; thus, there is a pressing need for new therapies for this disease. Genetic and small m ...

    Rearrangements of the MLL gene define a genetically distinct subset of acute leukemias with poor prognosis. Current treatment options are of limited effectiveness; thus, there is a pressing need for new therapies for this disease. Genetic and small molecule inhibitor studies have demonstrated that the histone methyltransferase DOT1L is required for the development and maintenance of MLL-rearranged leukemia in model systems. Here we describe the characterization of EPZ-5676, a potent and selective aminonucleoside inhibitor of DOT1L histone methyltransferase activity. The compound has an inhibition constant value of 80 pM, and demonstrates 37‚ÄČ000-fold selectivity over all other methyltransferases tested. In cellular studies, EPZ-5676 inhibited H3K79 methylation and MLL-fusion target gene expression and demonstrated potent cell killing that was selective for acute leukemia lines bearing MLL translocations. Continuous IV infusion of EPZ-5676 in a rat xenograft model of MLL-rearranged leukemia caused complete tumor regressions that were sustained well beyond the compound infusion period with no significant weight loss or signs of toxicity. EPZ-5676 is therefore a potential treatment of MLL-rearranged leukemia and is under clinical investigation.


    Organizational Affiliation

    Epizyme, Inc., 400 Technology Square, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EP6
Query on EP6

Download SDF File 
Download CCD File 
A
5'-[{cis-3-[2-(5-tert-butyl-1H-benzimidazol-2-yl)ethyl]cyclobutyl}(propan-2-yl)amino]-5'-deoxyadenosine
C30 H42 N8 O3
LXFOLMYKSYSZQS-LURJZOHASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EP6Ki: 0.1 nM (100) BINDINGDB
EP6IC50: 3 - 3.5 nM (100) BINDINGDB
EP6Ki: 0.08 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.183 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 154.430α = 90.00
b = 154.430β = 90.00
c = 47.520γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
Aimlessdata scaling
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-26 
  • Released Date: 2013-07-31 
  • Deposition Author(s): Jin, L.

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references