5JI6

Potent, Reversible MetAP2 Inhibitors via FBDD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of potent, reversible MetAP2 inhibitors via fragment based drug discovery and structure based drug design-Part 1.

Cheruvallath, Z.Tang, M.McBride, C.Komandla, M.Miura, J.Ton-Nu, T.Erikson, P.Feng, J.Farrell, P.Lawson, J.D.Vanderpool, D.Wu, Y.Dougan, D.R.Plonowski, A.Holub, C.Larson, C.

(2016) Bioorg.Med.Chem.Lett. 26: 2774-2778

  • DOI: 10.1016/j.bmcl.2016.04.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine aminopeptidase 2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. Pre-clinical and clinical studies suggest that MetAP2 inhibitors could be used as a novel treatment for obesi ...

    Methionine aminopeptidase 2 (MetAP2) is an enzyme that cleaves an N-terminal methionine residue from a number of newly synthesized proteins. Pre-clinical and clinical studies suggest that MetAP2 inhibitors could be used as a novel treatment for obesity. Herein we describe our use of fragment screening methods and structural biology to quickly identify and elaborate an indazole fragment into a series of reversible MetAP2 inhibitors with <10nM potency, excellent selectivity, and favorable in vitro safety profiles.


    Organizational Affiliation

    Medicinal Chemistry, Takeda California, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 2
A
369Homo sapiensMutation(s): 0 
Gene Names: METAP2 (MNPEP, P67EIF2)
EC: 3.4.11.18
Find proteins for P50579 (Homo sapiens)
Go to Gene View: METAP2
Go to UniProtKB:  P50579
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
6KN
Query on 6KN

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Download CCD File 
A
4-(3-methylpyridin-4-yl)-6-(trifluoromethyl)-1H-indazole
C14 H10 F3 N3
SERKGWYXQDCJCM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 88.962α = 90.00
b = 100.100β = 90.00
c = 99.469γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement
XFITdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description