4EKI

Crystal Structure of DOT1L in complex with EPZ004777


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 


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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 leukemia, is a required driver of leukemogenesis in this malignancy ...

    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 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QK (Subject of Investigation/LOI)
Query on 0QK

Download Ideal Coordinates CCD File 
B [auth A]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 H41 N7 O4
WXRGFPHDRFQODR-ICLZECGLSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0QK BindingDB:  4EKI Ki: min: 0.3, max: 300 (nM) from 2 assay(s)
Kd: 0.25 (nM) from 1 assay(s)
IC50: min: 0.4, max: 400 (nM) from 3 assay(s)
EC50: 9 (nM) from 1 assay(s)
PDBBind:  4EKI Kd: 0.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.053α = 90
b = 155.053β = 90
c = 48.452γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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