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

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.230 

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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 D Biol Crystallogr 62: 425-432

  • DOI: https://doi.org/10.1107/S0907444906003878
  • Primary Citation of Related Structures:  
    2EVC, 2EVM, 2EVO

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase
A, B
264Escherichia coliMutation(s): 0 
Gene Names: map
Find proteins for P0AE18 (Escherichia coli (strain K12))
Explore P0AE18 
Go to UniProtKB:  P0AE18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE18
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CT0 Binding MOAD:  2EVO IC50: 67 (nM) from 1 assay(s)
PDBBind:  2EVO IC50: 67 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.2α = 90
b = 63.4β = 108.5
c = 75.3γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
CrystalCleardata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description