1QXW

Crystal structure of Staphyloccocus aureus in complex with an aminoketone inhibitor 54135.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of staphylococcusaureus methionine aminopeptidase complexed with keto heterocycle and aminoketone inhibitors reveal the formation of a tetrahedral intermediate.

Douangamath, A.Dale, G.E.D'Arcy, A.Almstetter, M.Eckl, R.Frutos-Hoener, A.Henkel, B.Illgen, K.Nerdinger, S.Schulz, H.MacSweeney, A.Thormann, M.Treml, A.Pierau, S.Wadman, S.Oefner, C.

(2004) J Med Chem 47: 1325-1328

  • DOI: 10.1021/jm034188j
  • Primary Citation of Related Structures:  
    1QXW, 1QXZ, 1QXY

  • PubMed Abstract: 
  • High-resolution crystal structures of Staphylococcus aureus methionine aminopeptidase I in complex with various keto heterocycles and aminoketones were determined, and the intermolecular ligand interactions with the enzyme are reported. The compounds ...

    High-resolution crystal structures of Staphylococcus aureus methionine aminopeptidase I in complex with various keto heterocycles and aminoketones were determined, and the intermolecular ligand interactions with the enzyme are reported. The compounds are effective inhibitors of the S. aureus enzyme because of the formation of an uncleavable tetrahedral intermediate upon binding. The electron densities unequivocally show the enzyme-catalyzed transition-state analogue mimicking that for amide bond hydrolysis of substrates.


    Organizational Affiliation

    Morphochem AG, WRO-1055/388, Schwarzwaldallee 215, CH-4058 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
methionyl aminopeptidaseA252Staphylococcus aureusMutation(s): 0 
EC: 3.4.11.18
Find proteins for P0A078 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A078 
Go to UniProtKB:  P0A078
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M1C
Query on M1C

Download CCD File 
A
(3S)-3-AMINO-1-(CYCLOPROPYLAMINO)HEPTANE-2,2-DIOL
C10 H22 N2 O2
AYBDGNNJGBFOBQ-VIFPVBQESA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CO
Query on CO

Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M1CIC50:  7000   nM  Binding MOAD
M1CIC50 :  7000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.993α = 90
b = 76.843β = 104.19
c = 41.935γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance