6B41

Menin bound to M-525


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.252 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CJVClick on this verticalbar to view detailsBest fitted 7PRClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Design of the First-in-Class, Highly Potent Irreversible Inhibitor Targeting the Menin-MLL Protein-Protein Interaction.

Xu, S.Aguilar, A.Xu, T.Zheng, K.Huang, L.Stuckey, J.Chinnaswamy, K.Bernard, D.Fernandez-Salas, E.Liu, L.Wang, M.McEachern, D.Przybranowski, S.Foster, C.Wang, S.

(2018) Angew Chem Int Ed Engl 57: 1601-1605

  • DOI: https://doi.org/10.1002/anie.201711828
  • Primary Citation of Related Structures:  
    6B41

  • PubMed Abstract: 

    The structure-based design of M-525 as the first-in-class, highly potent, irreversible small-molecule inhibitor of the menin-MLL interaction is presented. M-525 targets cellular menin protein at sub-nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL-regulated gene expression in MLL leukemia cells. M-525 demonstrates high cellular specificity over non-MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co-crystal structure of M-525 in complex with menin firmly establish its mode of action. A single administration of M-525 effectively suppresses MLL-regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M-525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.


  • Organizational Affiliation

    Comprehensive Cancer and Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, 1600 Huron Parkway, Ann Arbor, MI, 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Menin550Homo sapiensMutation(s): 0 
Gene Names: MEN1SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens)
Explore O00255 
Go to UniProtKB:  O00255
PHAROS:  O00255
GTEx:  ENSG00000133895 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00255
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.252 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.92α = 90
b = 153.92β = 90
c = 81.618γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CJVClick on this verticalbar to view detailsBest fitted 7PRClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary