2GG9

Novel bacterial methionine aminopeptidase inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors.

Evdokimov, A.G.Pokross, M.Walter, R.L.Mekel, M.Barnett, B.L.Amburgey, J.Seibel, W.L.Soper, S.J.Djung, J.F.Fairweather, N.Diven, C.Rastogi, V.Grinius, L.Klanke, C.Siehnel, R.Twinem, T.Andrews, R.Curnow, A.

(2007) Proteins 66: 538-546

  • DOI: https://doi.org/10.1002/prot.21207
  • Primary Citation of Related Structures:  
    2GG0, 2GG2, 2GG3, 2GG5, 2GG7, 2GG8, 2GG9, 2GGB, 2GGC

  • PubMed Abstract: 

    In this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N-terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole-diamines. Atomic-resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding.


  • Organizational Affiliation

    Structural Biology Core Facility, The Procter & Gamble Pharmaceuticals, Mason, Ohio 45040, USA. artem@xtals.org


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase263Escherichia coli K-12Mutation(s): 0 
Gene Names: map
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
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
U16 PDBBind:  2GG9 IC50: 3500 (nM) from 1 assay(s)
BindingDB:  2GG9 IC50: 3500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.131α = 90
b = 63.29β = 109.71
c = 52.513γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description