2EVM

crystal structure of methionine aminopeptidase in complex with 5-(2,5-dichlorophenyl)furan-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.235 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase264Escherichia coliMutation(s): 0 
EC: 3.4.11.18
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FC2 BindingDB:  2EVM IC50: min: 693, max: 1.73e+5 (nM) from 4 assay(s)
PDBBind:  2EVM IC50: 693 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.8α = 90
b = 60.2β = 104.5
c = 50.4γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
AMoREphasing
CNSrefinement
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