MLL1 SET N3861I/Q3867L bound to inhibitor 14 (TC-5139)

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of Potent Small-Molecule Inhibitors of MLL Methyltransferase.

Chern, T.R.Liu, L.Petrunak, E.Stuckey, J.A.Wang, M.Bernard, D.Zhou, H.Lee, S.Dou, Y.Wang, S.

(2020) ACS Med Chem Lett 11: 1348-1352

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00229
  • Primary Citation of Related Structures:  
    6U9K, 6U9M, 6U9N, 6U9R

  • PubMed Abstract: 

    The mixed-lineage leukemia (MLL) protein, also known as MLL1, is a lysine methyltransferase specifically responsible for methylation of histone 3 lysine 4. MLL has been pursued as an attractive therapeutic target for the treatment of acute leukemia carrying the MLL fusion gene or MLL leukemia. Herein, we report the design, synthesis, and evaluation of an S -adenosylmethionine-based focused chemical library which led to the discovery of potent small-molecule inhibitors directly targeting the MLL SET domain. Determination of cocrystal structures for a number of these MLL inhibitors reveals that they adopt a unique binding mode that locks the MLL SET domain in an open, inactive conformation.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Department of Internal Medicine, Department of Pharmacology, Department of Pathology, and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase
A, B
158Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens)
Explore Q03164 
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03164
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
Q34 Binding MOAD:  6U9N IC50: 55.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.629α = 90
b = 54.629β = 90
c = 105.832γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description