5JFR

Potent, Reversible MetAP2 Inhibitors via Fragment Based Drug Discovery


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of potent, reversible MetAP2 inhibitors via fragment based drug discovery and structure based drug design-Part 2.

McBride, C.Cheruvallath, Z.Komandla, M.Tang, M.Farrell, P.Lawson, J.D.Vanderpool, D.Wu, Y.Dougan, D.R.Plonowski, A.Holub, C.Larson, C.

(2016) Bioorg Med Chem Lett 26: 2779-2783

  • DOI: https://doi.org/10.1016/j.bmcl.2016.04.072
  • Primary Citation of Related Structures:  
    5JFR

  • PubMed Abstract: 

    Methionine aminopeptidase-2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. This step is required before they will fold or function correctly. Pre-clinical and clinical studies with a MetAP2 inhibitor suggest that they could be used as a novel treatment for obesity. Herein we describe the discovery of a series of pyrazolo[4,3-b]indoles as reversible MetAP2 inhibitors. A fragment-based drug discovery (FBDD) approach was used, beginning with the screening of fragment libraries to generate hits with high ligand-efficiency (LE). An indazole core was selected for further elaboration, guided by structural information. SAR from the indazole series led to the design of a pyrazolo[4,3-b]indole core and accelerated knowledge-based fragment growth resulted in potent and efficient MetAP2 inhibitors, which have shown robust and sustainable body weight loss in DIO mice when dosed orally.


  • Organizational Affiliation

    Medicinal Chemistry, Takeda California, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 2369Homo sapiensMutation(s): 0 
Gene Names: METAP2MNPEPP67EIF2
EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens)
Explore P50579 
Go to UniProtKB:  P50579
PHAROS:  P50579
GTEx:  ENSG00000111142 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50579
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
6KP Binding MOAD:  5JFR IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.644α = 90
b = 100.816β = 90
c = 99.445γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references