Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78589.85 
• Atom Count: 5009 
• Residue Count: 668 
• Unique protein chains: 1

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]

• DOI: 10.2210/pdb5MW4/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-01-18 Released: 2017-03-22 
• Deposition Author(s): Be, C., Koch, E., Gaul, C., Stauffer, F., Moebitz, H., Scheufler, C.

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Experimental Data Snapshot

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

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

• PubMed: 28337327 
• DOI: 10.1021/acsmedchemlett.6b00519
• Primary Citation of Related Structures:  
  5MW3, 5MVS


• 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. 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.

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Organizational Affiliation: 

Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase, H3 lysine-79 specific	A, B	334	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
5JU	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
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 158.360	α = 90.00
b = 158.360	β = 90.00
c = 74.590	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data reduction
BUSTER	refinement
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-01-18 
• Released Date: 2017-03-22 
• Deposition Author(s): Be, C., Koch, E., Gaul, C., Stauffer, F., Moebitz, H., Scheufler, C.

Revision History 

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