5DTM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A, B
334Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens)
Go to UniProtKB:  Q8TEK3
PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5F4
Query on 5F4

Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.559α = 90
b = 158.559β = 90
c = 73.396γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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