4OG8

Human menin with bound inhibitor MIV-6R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • 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 


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