5VFC

WDR5 bound to inhibitor MM-589


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 60: 4818-4839

  • DOI: 10.1021/acs.jmedchem.6b01796
  • Primary Citation of Related Structures:  
    4GMB, 5VFC

  • 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 IC 50 value of 0 ...

    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 IC 50 value of 0.90 nM (K i value <1 nM) and inhibits the MLL H3K4 methyltransferase (HMT) activity with an IC 50 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5A311Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
PHAROS:  P61964
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9BA (Subject of Investigation/LOI)
Query on 9BA

Download Ideal Coordinates CCD File 
B [auth A]N-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide
C28 H44 N8 O5
ZAIPJVQTYUSDTG-LDFBIXNTSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9BA Binding MOAD:  5VFC IC50: 0.9 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002270 (9BA)
Query on PRD_002270
B [auth A]inhibitor MM-589Cyclic peptide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.348α = 90
b = 58.559β = 96.16
c = 56.801γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-07 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Stuckey, J.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA177307

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence