6TE6 | pdb_00006te6

Crystal structure of Dot1L in complex with an inhibitor (compound 3).

• PDB DOI: https://doi.org/10.2210/pdb6TE6/pdb

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


• Deposited: 2019-11-11 Released: 2019-12-11 
• Deposition Author(s): Scheufler, C., Stauffer, F., Be, C., Moebitz, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.201 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

New Potent DOT1L Inhibitors forin VivoEvaluation in Mouse.

Stauffer, F., Weiss, A., Scheufler, C., Mobitz, H., Ragot, C., Beyer, K.S., Calkins, K., Guthy, D., Kiffe, M., Van Eerdenbrugh, B., Tiedt, R., Gaul, C.

(2019) ACS Med Chem Lett 10: 1655-1660

• PubMed: 31857842 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00452
• Primary Citation Related Structures: 
  6TE6, 6TEL, 6TEN


• PubMed Abstract: 
  

  In MLL-rearranged cancer cells, disruptor of telomeric silencing 1-like protein (DOT1L) is aberrantly recruited to ectopic loci leading to local hypermethylation of H3K79 and consequently misexpression of leukemogenic genes. A structure-guided optimization of a HTS hit led to the discovery of DOT1L inhibitors with subnanomolar potency, allowing testing of the therapeutic principle of DOT1L inhibition in a preclinical mouse tumor xenograft model. Compounds displaying good exposure in mouse and nanomolar inhibition of target gene expression in cells were obtained and tested in vivo.

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Organizational Affiliation: 
• Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.85 kDa 
• Atom Count: 5,623 
• Modeled Residue Count: 642 
• 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
N4W (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine C23 H20 Cl N5 O2 S JZZKDASEJHKEGM-QFIPXVFZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N4W	BindingDB:  6TE6	IC50: 270 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.201 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.54	α = 90
b = 158.54	β = 90
c = 74.23	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Scheufler, C., Stauffer, F., Be, C., Moebitz, H.

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2020-03-11
  Changes: Data collection
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description