5LYX

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 5-((R)-1-[1,2,4]Triazolo[1,5-a]pyrimidin-7-yl-pyrrolidin-2-ylmethoxy)-isoquinoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel reversible methionine aminopeptidase-2 (MetAP-2) inhibitors based on purine and related bicyclic templates.

Heinrich, T.Buchstaller, H.P.Cezanne, B.Rohdich, F.Bomke, J.Friese-Hamim, M.Krier, M.Knochel, T.Musil, D.Leuthner, B.Zenke, F.

(2017) Bioorg. Med. Chem. Lett. 27: 551-556

  • DOI: 10.1016/j.bmcl.2016.12.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The natural product fumagillin 1 and derivatives like TNP-470 2 or beloranib 3 bind to methionine aminopeptidase 2 (MetAP-2) irreversibly. This enzyme is critical for protein maturation and plays a key role in angiogenesis. In this paper we describe ...

    The natural product fumagillin 1 and derivatives like TNP-470 2 or beloranib 3 bind to methionine aminopeptidase 2 (MetAP-2) irreversibly. This enzyme is critical for protein maturation and plays a key role in angiogenesis. In this paper we describe the synthesis, MetAP-2 binding affinity and structural analysis of reversible MetAP-2 inhibitors. Optimization of enzymatic activity of screening hit 10 (IC50: 1μM) led to the most potent compound 27 (IC50: 0.038μM), with a concomitant improvement in LLE from 2.1 to 4.2. Structural analysis of these MetAP-2 inhibitors revealed an unprecedented conformation of the His339 side-chain imidazole ring being co-planar sandwiched between the imidazole of His331 and the aryl-ether moiety, which is bound to the purine scaffold. Systematic alteration and reduction of H-bonding capability of this metal binding moiety induced an unexpected 180° flip for the triazolo[1,5-a]pyrimdine bicyclic template.


    Organizational Affiliation

    Discovery Technologies, Merck KGaA, Frankfurter Str. 250, D-64293 Darmstadt, Germany. Electronic address: timo.heinrich@merckgroup.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 2
A
378Homo 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 2 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
7BF
Query on 7BF

Download SDF File 
Download CCD File 
A
5-[[(2~{R})-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methoxy]isoquinoline
C19 H18 N6 O
UCCCEISNAUTIDA-OAHLLOKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.215α = 90.00
b = 99.944β = 90.00
c = 100.930γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTER-TNTrefinement
XDSdata reduction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release