4GQ4

Human menin with bound inhibitor MI-2-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0RT
Query on 0RT

Download Ideal Coordinates CCD File 
B [auth A]4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine
C17 H20 F3 N5 S2
SFDROHXKTATJBI-UHFFFAOYSA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
H [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
O [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
0RT BindingDB:  4GQ4 IC50: min: 46, max: 190 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.044α = 90
b = 80.16β = 90
c = 124.812γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0RTClick on this verticalbar to view details

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: 2024-02-28
    Changes: Data collection, Database references, Derived calculations