2EVO

crystal structure of methionine amino peptidase in complex with N-cyclopentyl-N-(thiazol-2-yl)oxalamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of metalloform-selective inhibition of methionine aminopeptidase.

Xie, S.X.Huang, W.J.Ma, Z.Q.Huang, M.Hanzlik, R.P.Ye, Q.Z.

(2006) Acta Crystallogr.,Sect.D 62: 425-432

  • DOI: 10.1107/S0907444906003878
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One of the challenges in the development of methionine aminopeptidase (MetAP) inhibitors as antibacterial and anticancer agents is to define the metal ion actually used by MetAP in vivo and to discover MetAP inhibitors that can inhibit the metallofor ...

    One of the challenges in the development of methionine aminopeptidase (MetAP) inhibitors as antibacterial and anticancer agents is to define the metal ion actually used by MetAP in vivo and to discover MetAP inhibitors that can inhibit the metalloform that is relevant in vivo. Two distinct classes of novel nonpeptidic MetAP inhibitors that are not only potent but also highly selective for either the Mn(II) or Co(II) form have been identified. Three crystal structures of Escherichia coli MetAP complexed with the metalloform-selective inhibitors 5-(2,5-dichlorophenyl)furan-2-carboxylic acid (2), 5-[2-(trifluoromethyl)phenyl]furan-2-carboxylic acid (3) and N-cyclopentyl-N-(thiazol-2-yl)oxalamide (4) have been solved and analysis of these structures has revealed the structural basis for their metalloform-selective inhibition. The Mn(II)-form selective inhibitors (2) and (3) both use their carboxylate group to coordinate with the two Mn(II) ions at the dinuclear metal site and both adopt a non-coplanar conformation for the two aromatic rings. The unique coordination geometry of these inhibitors may determine their Mn(II)-form selectivity. In contrast, the Co(II)-form selective inhibitor (4) recruits an unexpected third metal ion, forming a trimetallic enzyme-metal-inhibitor complex. Thus, an important factor in the selectivity of (4) for the Co(II) form may be a consequence of a greater preference for a softer N,O-donor ligand for the softer Co(II).


    Organizational Affiliation

    High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase
A, B
264Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: map
EC: 3.4.11.18
Find proteins for P0AE18 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE18
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CT0
Query on CT0

Download SDF File 
Download CCD File 
A, B
N1-CYCLOPENTYL-N2-(THIAZOL-2-YL)OXALAMIDE
C10 H13 N3 O2 S
BJHPYHUDDCVBNG-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CT0IC50: 67 nM BINDINGMOAD
CT0IC50: 67 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.200α = 90.00
b = 63.400β = 108.50
c = 75.300γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
XDSdata reduction
CrystalCleardata reduction
CrystalCleardata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-10-31 
  • Released Date: 2006-03-28 
  • Deposition Author(s): Huang, W.-J.

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance