Aquifex aeolicus KDO8PS in complex with cadmium and APP, a bisubstrate inhibitor

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-Based Design of Novel Inhibitors of 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase.

Xu, X.Wang, J.Grison, C.Petek, S.Coutrot, P.Birck, M.R.Woodard, R.W.Gatti, D.L.

(2003) Drug Des Discov 18: 91-99

  • Primary Citation of Related Structures:  
    1PCK, 1PCW, 1PE1

  • PubMed Abstract: 

    3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) is the phosphorylated precursor of KDO, an essential sugar of the lipopolysaccharide of Gram negative bacteria. KDO8P is produced by a specific synthase (KDO8PS) by condensing arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP), with release of inorganic phosphate. As KDO8PS is present in bacteria and plants, but not in mammalian cells, and mutations that inactivate KDO8PS also block cell replication, KDO8PS is a promising target for the design of new antimicrobials that act by blocking lipopolysaccharide biosynthesis. Previous studies have shown that a compound mimicking an intermediate of the condensation reaction is a good ligand and a powerful inhibitor. Here we report on the crystallographic investigation of the binding to KDO8PS of new derivatives of this original inhibitor. The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, 48201 USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase
A, B
267Aquifex aeolicusMutation(s): 0 
Gene Names: KDSA OR AQ_085
Find proteins for O66496 (Aquifex aeolicus (strain VF5))
Explore O66496 
Go to UniProtKB:  O66496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66496
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.48α = 90
b = 84.48β = 90
c = 159.07γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description