4GM8

Crystal structure of human WD repeat domain 5 with compound MM-102


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-affinity, small-molecule peptidomimetic inhibitors of MLL1/WDR5 protein-protein interaction.

Karatas, H.Townsend, E.C.Cao, F.Chen, Y.Bernard, D.Liu, L.Lei, M.Dou, Y.Wang, S.

(2013) J.Am.Chem.Soc. 135: 669-682

  • DOI: 10.1021/ja306028q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mixed lineage leukemia 1 (MLL1) is a histone H3 lysine 4 (H3K4) methyltransferase, and targeting the MLL1 enzymatic activity has been proposed as a novel therapeutic strategy for the treatment of acute leukemia harboring MLL1 fusion proteins. The MLL ...

    Mixed lineage leukemia 1 (MLL1) is a histone H3 lysine 4 (H3K4) methyltransferase, and targeting the MLL1 enzymatic activity has been proposed as a novel therapeutic strategy for the treatment of acute leukemia harboring MLL1 fusion proteins. The MLL1/WDR5 protein-protein interaction is essential for MLL1 enzymatic activity. In the present study, we designed a large number of peptidomimetics to target the MLL1/WDR5 interaction based upon -CO-ARA-NH-, the minimum binding motif derived from MLL1. Our study led to the design of high-affinity peptidomimetics, which bind to WDR5 with K(i) < 1 nM and function as potent antagonists of MLL1 activity in a fully reconstituted in vitro H3K4 methyltransferase assay. Determination of co-crystal structures of two potent peptidomimetics in complex with WDR5 establishes their structural basis for high-affinity binding to WDR5. Evaluation of one such peptidomimetic, MM-102, in bone marrow cells transduced with MLL1-AF9 fusion construct shows that the compound effectively decreases the expression of HoxA9 and Meis-1, two critical MLL1 target genes in MLL1 fusion protein mediated leukemogenesis. MM-102 also specifically inhibits cell growth and induces apoptosis in leukemia cells harboring MLL1 fusion proteins. Our study provides the first proof-of-concept for the design of small-molecule inhibitors of the WDR5/MLL1 protein-protein interaction as a novel therapeutic approach for acute leukemia harboring MLL1 fusion proteins.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A, B, C, D
313Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MM-102
E, F, G, H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000894
Query on PRD_000894
EMM-102Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.861α = 90.00
b = 106.478β = 90.35
c = 120.719γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASESphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release