4GMB | pdb_00004gmb

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4GMB

This is version 2.0 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: https://doi.org/10.1021/acs.jmedchem.6b01796
  • Primary Citation 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 0.90 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.

Macromolecule Content 

  • Total Structure Weight: 35.02 kDa 
  • Atom Count: 2,481 
  • Modeled Residue Count: 312 
  • Deposited Residue Count: 318 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5313Homo 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
GTEx:  ENSG00000196363 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MM-402B [auth E]5N/AMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0XQ
Query on 0XQ
B [auth E]D-PEPTIDE LINKINGC9 H20 N2 O2

--

ABA
Query on ABA
B [auth E]L-PEPTIDE LINKINGC4 H9 N O2ALA
PG9
Query on PG9
B [auth E]D-PEPTIDE LINKINGC8 H9 N O2

--

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.297α = 90
b = 50.837β = 90
c = 137.845γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2023-09-13
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations