4I80

Crystal structure of human menin in complex with a high-affinity macrocyclic peptidomimetics


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-Based Design of High-Affinity Macrocyclic Peptidomimetics to Block the Menin-Mixed Lineage Leukemia 1 (MLL1) Protein-Protein Interaction.

Zhou, H.Liu, L.Huang, J.Bernard, D.Karatas, H.Navarro, A.Lei, M.Wang, S.

(2013) J.Med.Chem. 56: 1113-1123

  • DOI: 10.1021/jm3015298

  • PubMed Abstract: 
  • Menin is an essential oncogenic cofactor for mixed lineage leukemia 1 (MLL1)-mediated leukemogenesis through its direct interaction with MLL1. Targeting the menin-MLL1 protein-protein interaction represents a promising strategy to block MLL1-mediated ...

    Menin is an essential oncogenic cofactor for mixed lineage leukemia 1 (MLL1)-mediated leukemogenesis through its direct interaction with MLL1. Targeting the menin-MLL1 protein-protein interaction represents a promising strategy to block MLL1-mediated leukemogenesis. Employing a structure-based approach and starting from a linear MLL1 octapeptide, we have designed a class of potent macrocyclic peptidomimetic inhibitors of the menin-MLL1 interaction. The most potent macrocyclic peptidomimetic (MCP-1), 34, binds to menin with a K(i) value of 4.7 nM and is >600 times more potent than the corresponding acyclic peptide. Compound 34 is also less peptide-like and has a lower molecular weight than the initial MLL1 peptide. Therefore, compound 34 serves as a promising lead structure for the design of potent and cell-permeable inhibitors of the menin-MLL1 interaction.


    Organizational Affiliation

    Comprehensive Cancer Center and Department of Internal Medicine, University of Michigan , 1500 E. Medical Center Drive, Ann Arbor, Michigan 48109-0934, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Menin
A
550Homo sapiensMutation(s): 0 
Gene Names: MEN1 (SCG2)
Find proteins for O00255 (Homo sapiens)
Go to Gene View: MEN1
Go to UniProtKB:  O00255
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
macrocyclic peptidomimetic
B
9N/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_000967
Query on PRD_000967
Bmacrocyclic peptidomimeticPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.379α = 90.00
b = 141.379β = 90.00
c = 92.879γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-12-01 
  • Released Date: 2013-03-06 
  • Deposition Author(s): Huang, J., Lei, M.

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Derived calculations
  • Version 1.2: 2017-06-21
    Type: Database references, Source and taxonomy
  • Version 1.3: 2017-11-15
    Type: Refinement description