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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77507.46 
• Atom Count: 5163 
• Residue Count: 668 
• Unique protein chains: 1

5DTM

Crystal structure of Dot1L in complex with inhibitor CPD1 [4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide]

• DOI: 10.2210/pdb5DTM/pdb

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


• Deposited: 2015-09-18 Released: 2016-06-15 
• Deposition Author(s): Scheufler, C., Be, C., Moebitz, H., Stauffer, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 

Literature

Optimization of a Fragment-Based Screening Hit toward Potent DOT1L Inhibitors Interacting in an Induced Binding Pocket.

Scheufler, C., Mobitz, H., Gaul, C., Ragot, C., Be, C., Fernandez, C., Beyer, K.S., Tiedt, R., Stauffer, F.

(2016) Acs Med.Chem.Lett. 7: 730-734

• PubMed: 27563394 
• DOI: 10.1021/acsmedchemlett.6b00168
• Primary Citation of Related Structures:  
  5DTR, 5DTQ


• PubMed Abstract: 
  

Mixed lineage leukemia (MLL) gene rearrangement induces leukemic transformation by ectopic recruitment of disruptor of telomeric silencing 1-like protein (DOT1L), a lysine histone methyltransferase, leading to local hypermethylation of H3K79 and misexpression of genes (including HoxA), which drive the leukemic phenotype. A weak fragment-based screening hit identified by SPR was cocrystallized with DOT1L and optimized using structure-based ligand optimization to yield compound 8 (IC50 = 14 nM). This series of inhibitors is structurally not related to cofactor SAM and is not interacting within the SAM binding pocket but induces a pocket adjacent to the SAM binding site.

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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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
5F4	A, B	4-(2,6-dichlorobenzoyl)-N-methyl-1H-pyrrole-2-carboxamide C13 H10 Cl2 N2 O2 IMCVPHRDALQWTJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 158.559	α = 90.00
b = 158.559	β = 90.00
c = 73.396	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-18 
• Released Date: 2016-06-15 
• Deposition Author(s): Scheufler, C., Be, C., Moebitz, H., Stauffer, F.

Revision History 

• Version 1.0: 2016-06-15
  Type: Initial release
• Version 1.1: 2016-09-07
  Type: Database references