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 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4HRA

  • 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 molecule inhibitor studies have demonstrated that the histone methyltransferase DOT1L is required for the development and maintenance of MLL-rearranged leukemia in model systems ...

    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 37 000-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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificA425Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens)
Explore Q8TEK3 
Go to UniProtKB:  Q8TEK3
PHAROS:  Q8TEK3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EP6 (Subject of Investigation/LOI)
Query on EP6

Download Ideal Coordinates CCD File 
B [auth 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EP6 BindingDB:  4HRA Ki: min: 0.01, max: 0.08 (nM) from 2 assay(s)
IC50: min: 0.1, max: 52 (nM) from 7 assay(s)
PDBBind:  4HRA Ki: 0.08 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.43α = 90
b = 154.43β = 90
c = 47.52γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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