5DTM

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

• PDB DOI: https://doi.org/10.2210/pdb5DTM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.20 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1021/acsmedchemlett.6b00168
• Primary Citation of Related Structures:  
  5DTM, 5DTQ, 5DTR


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.51 kDa 
• Atom Count: 5,626 
• Modelled Residue Count: 638 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 (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 GTEx:  ENSG00000104885

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
5F4	BindingDB:  5DTM	Kd: 5.00e+4 (nM) from 1 assay(s)
		IC50: 3.20e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.559	α = 90
b = 158.559	β = 90
c = 73.396	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description