4WVL

Structure-Guided DOT1L Probe Optimization by Label-Free Ligand Displacement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Guided DOT1L Probe Optimization by Label-Free Ligand Displacement.

Yi, J.S.Federation, A.J.Qi, J.Dhe-Paganon, S.Hadler, M.Xu, X.St Pierre, R.Varca, A.C.Wu, L.Marineau, J.J.Smith, W.B.Souza, A.Chory, E.J.Armstrong, S.A.Bradner, J.E.

(2015) Acs Chem.Biol. 10: 667-674

  • DOI: 10.1021/cb500796d

  • PubMed Abstract: 
  • The DOT1L lysine methyltransferase has emerged as a validated therapeutic target in MLL-rearranged (MLLr) acute leukemias. Although S-adenosylmethionine competitive inhibitors have demonstrated pharmacological proof-of-principle in MLLr-leukemia, the ...

    The DOT1L lysine methyltransferase has emerged as a validated therapeutic target in MLL-rearranged (MLLr) acute leukemias. Although S-adenosylmethionine competitive inhibitors have demonstrated pharmacological proof-of-principle in MLLr-leukemia, these compounds require further optimization to improve cellular potency and pharmacokinetic stability. Limiting DOT1L inhibitor discovery and ligand optimization have been complex biochemical methods often using radionucleotides and cellular methods requiring prolonged culture. We therefore developed a new suite of assay technologies that allows comparative assessment of chemical tools for DOT1L in a miniaturized format. Coupling these assays with structural information, we developed new insights into DOT1L ligand binding and identified several functionalized probes with increased cellular potency (IC50 values ∼10 nM) and excellent selectivity for DOT1L. Together these assay technologies define a platform capability for discovery and optimization of small-molecule DOT1L inhibitors.


    Organizational Affiliation

    †Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A
347Homo 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 4 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
3US
Query on 3US

Download SDF File 
Download CCD File 
A
N-[4-(acetylamino)butyl]-5'-[(3-{[(4-tert-butylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine
C33 H51 N9 O5
UMDWALJSYFZDHM-QWOIFIOOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.168 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 151.104α = 90.00
b = 151.104β = 90.00
c = 53.387γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references
  • Version 1.3: 2015-08-26
    Type: Data collection