4GMB

Crystal structure of human WD repeat domain 5 with compound MM-402


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.781 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction.

Karatas, H.Li, Y.Liu, L.Ji, J.Lee, S.Chen, Y.Yang, J.Huang, L.Bernard, D.Xu, J.Townsend, E.C.Cao, F.Ran, X.Li, X.Wen, B.Sun, D.Stuckey, J.A.Lei, M.Dou, Y.Wang, S.

(2017) J. Med. Chem. --: --

  • DOI: 10.1021/acs.jmedchem.6b01796
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report herein the design, synthesis, and evaluation of macrocyclic peptidomimetics that bind to WD repeat domain 5 (WDR5) and block the WDR5-mixed lineage leukemia (MLL) protein-protein interaction. Compound 18 (MM-589) binds to WDR5 with an IC50 ...

    We report herein the design, synthesis, and evaluation of macrocyclic peptidomimetics that bind to WD repeat domain 5 (WDR5) and block the WDR5-mixed lineage leukemia (MLL) protein-protein interaction. Compound 18 (MM-589) binds to WDR5 with an IC50 value of 0.90 nM (Ki value <1 nM) and inhibits the MLL H3K4 methyltransferase (HMT) activity with an IC50 value of 12.7 nM. Compound 18 potently and selectively inhibits cell growth in human leukemia cell lines harboring MLL translocations and is >40 times better than the previously reported compound MM-401. Cocrystal structures of 16 and 18 complexed with WDR5 provide structural basis for their high affinity binding to WDR5. Additionally, we have developed and optimized a new AlphaLISA-based MLL HMT functional assay to facilitate the functional evaluation of these designed compounds. Compound 18 represents the most potent inhibitor of the WDR5-MLL interaction reported to date, and further optimization of 18 may yield a new therapy for acute leukemia.


    Organizational Affiliation

    Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A
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-402
E
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_000896
Query on PRD_000896
EMM-402Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.781 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.297α = 90.00
b = 50.837β = 90.00
c = 137.845γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references