4GQ6 | pdb_00004gq6

Human menin in complex with MLL peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.189 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4GQ6

This is version 1.3 of the entry. See complete history

Literature

Structural insights into inhibition of the bivalent menin-MLL interaction by small molecules in leukemia.

Shi, A.Murai, M.J.He, S.Lund, G.Hartley, T.Purohit, T.Reddy, G.Chruszcz, M.Grembecka, J.Cierpicki, T.

(2012) Blood 120: 4461-4469

  • DOI: https://doi.org/10.1182/blood-2012-05-429274
  • Primary Citation Related Structures: 
    4GPQ, 4GQ3, 4GQ4, 4GQ6

  • PubMed Abstract: 

    Menin functions as a critical oncogenic cofactor of mixed lineage leukemia (MLL) fusion proteins in the development of acute leukemias, and inhibition of the menin interaction with MLL fusion proteins represents a very promising strategy to reverse their oncogenic activity. MLL interacts with menin in a bivalent mode involving 2 N-terminal fragments of MLL. In the present study, we reveal the first high-resolution crystal structure of human menin in complex with a small-molecule inhibitor of the menin-MLL interaction, MI-2. The structure shows that the compound binds to the MLL pocket in menin and mimics the key interactions of MLL with menin. Based on the menin-MI-2 structure, we developed MI-2-2, a compound that binds to menin with low nanomolar affinity (K(d) = 22nM) and very effectively disrupts the bivalent protein-protein interaction between menin and MLL. MI-2-2 demonstrated specific and very pronounced activity in MLL leukemia cells, including inhibition of cell proliferation, down-regulation of Hoxa9 expression, and differentiation. Our results provide the rational and essential structural basis to design next generation of inhibitors for effective targeting of the menin-MLL interaction in leukemia and demonstrate a proof of concept that inhibition of complex multivalent protein-protein interactions can be achieved by a small-molecule inhibitor.


  • Organizational Affiliation
    • Department of Pathology, University of Michigan, Ann Arbor, MI, USA.

Macromolecule Content 

  • Total Structure Weight: 56.74 kDa 
  • Atom Count: 4,321 
  • Modeled Residue Count: 479 
  • Deposited Residue Count: 501 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Menin489Homo sapiensMutation(s): 1 
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
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase MLL12Homo sapiensMutation(s): 0 
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens)
Explore Q03164 
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03164
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.189 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.601α = 90
b = 80.056β = 90
c = 124.551γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Other
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations