4OG8

Human menin with bound inhibitor MIV-6R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2SFClick on this verticalbar to view detailsBest fitted PGAClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction.

He, S.Senter, T.J.Pollock, J.Han, C.Upadhyay, S.K.Purohit, T.Gogliotti, R.D.Lindsley, C.W.Cierpicki, T.Stauffer, S.R.Grembecka, J.

(2014) J Med Chem 57: 1543-1556

  • DOI: https://doi.org/10.1021/jm401868d
  • Primary Citation of Related Structures:  
    4OG3, 4OG4, 4OG5, 4OG6, 4OG7, 4OG8

  • PubMed Abstract: 

    The protein-protein interaction (PPI) between menin and mixed lineage leukemia (MLL) plays a critical role in acute leukemias, and inhibition of this interaction represents a new potential therapeutic strategy for MLL leukemias. We report development of a novel class of small-molecule inhibitors of the menin-MLL interaction, the hydroxy- and aminomethylpiperidine compounds, which originated from HTS of ∼288000 small molecules. We determined menin-inhibitor co-crystal structures and found that these compounds closely mimic all key interactions of MLL with menin. Extensive crystallography studies combined with structure-based design were applied for optimization of these compounds, resulting in MIV-6R, which inhibits the menin-MLL interaction with IC50 = 56 nM. Treatment with MIV-6 demonstrated strong and selective effects in MLL leukemia cells, validating specific mechanism of action. Our studies provide novel and attractive scaffold as a new potential therapeutic approach for MLL leukemias and demonstrate an example of PPI amenable to inhibition by small molecules.


  • Organizational Affiliation

    Department of Pathology, University of Michigan , Ann Arbor, 1150 West Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Menin489Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2SF
Query on 2SF

Download Ideal Coordinates CCD File 
C [auth A]4-(3-{4-[(R)-amino(cyclopentyl)phenylmethyl]piperidin-1-yl}propoxy)benzonitrile
C27 H35 N3 O
AUWUGRCKTQSGJY-HHHXNRCGSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGA
Query on PGA

Download Ideal Coordinates CCD File 
I [auth A]2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
TBF
Query on TBF

Download Ideal Coordinates CCD File 
B [auth A],
L [auth A]
TERT-BUTYL FORMATE
C5 H10 O2
RUPAXCPQAAOIPB-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
H [auth A],
J [auth A],
K [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2SF BindingDB:  4OG8 Ki: 58 (nM) from 1 assay(s)
Kd: min: 85, max: 1.10e+5 (nM) from 2 assay(s)
IC50: min: 56, max: 185 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.176 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.782α = 90
b = 80.224β = 90
c = 124.691γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

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 2SFClick on this verticalbar to view detailsBest fitted PGAClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description