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 

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 D Biol Crystallogr 62: 425-432

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

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine aminopeptidaseA264Escherichia coliMutation(s): 0 
EC: 3.4.11.18
Find proteins for P0AE18 (Escherichia coli (strain K12))
Explore P0AE18 
Go to UniProtKB:  P0AE18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FC2
Query on FC2

Download CCD File 
A
5-(2,5-DICHLOROPHENYL)-2-FUROIC ACID
C11 H6 Cl2 O3
ATAZLMGGQQLRBC-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FC2IC50:  693   nM  BindingDB
FC2IC50:  173000   nM  BindingDB
FC2IC50:  84000   nM  BindingDB
FC2IC50 :  693   nM  PDBBind
FC2IC50:  693   nM  Binding MOAD
FC2IC50:  126000   nM  BindingDB
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

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance