5MW4

Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent, Selective, and Structurally Novel Dot1L Inhibitors by a Fragment Linking Approach.

Mobitz, H.Machauer, R.Holzer, P.Vaupel, A.Stauffer, F.Ragot, C.Caravatti, G.Scheufler, C.Fernandez, C.Hommel, U.Tiedt, R.Beyer, K.S.Chen, C.Zhu, H.Gaul, C.

(2017) ACS Med Chem Lett 8: 338-343

  • DOI: 10.1021/acsmedchemlett.6b00519
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Misdirected catalytic activity of histone methyltransferase Dot1L is believed to be causative for a subset of highly aggressive acute leukemias. Targeting the catalytic domain of Dot1L represents a potential therapeutic approach for these leukemias. ...

    Misdirected catalytic activity of histone methyltransferase Dot1L is believed to be causative for a subset of highly aggressive acute leukemias. Targeting the catalytic domain of Dot1L represents a potential therapeutic approach for these leukemias. In the context of a comprehensive Dot1L hit finding strategy, a knowledge-based virtual screen of the Dot1L SAM binding pocket led to the discovery of 2, a non-nucleoside fragment mimicking key interactions of SAM bound to Dot1L. Fragment linking of 2 and 3, an induced back pocket binder identified in earlier studies, followed by careful ligand optimization led to the identification of 7, a highly potent, selective and structurally novel Dot1L inhibitor.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A, B
334Homo 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
5JU
Query on 5JU

Download SDF File 
Download CCD File 
A, B
N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide
C32 H36 Cl N9 O2 S
BUHUWDQAOUQQHQ-JOCHJYFZSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 158.360α = 90.00
b = 158.360β = 90.00
c = 74.590γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references