3V7R

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Selective inhibition of biotin protein ligase from Staphylococcus aureus.

Soares da Costa, T.P.Tieu, W.Yap, M.Y.Pendini, N.R.Polyak, S.W.Sejer Pedersen, D.Morona, R.Turnidge, J.D.Wallace, J.C.Wilce, M.C.Booker, G.W.Abell, A.D.

(2012) J Biol Chem 287: 17823-17832

  • DOI: https://doi.org/10.1074/jbc.M112.356576
  • Primary Citation of Related Structures:  
    3V7C, 3V7R, 3V7S, 3V8J, 3V8K, 3V8L, 4DQ2

  • PubMed Abstract: 

    There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.


  • Organizational Affiliation

    School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin ligase329Staphylococcus aureus A9781Mutation(s): 0 
Gene Names: SAOG_00031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
32G
Query on 32G

Download Ideal Coordinates CCD File 
B [auth A](3aS,4S,6aR)-4-(5-{1-[4-(6-amino-9H-purin-9-yl)butyl]-1H-1,2,3-triazol-4-yl}pentyl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one
C21 H30 N10 O S
GCOZLSRXMOWRSO-ULQDDVLXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
32G BindingDB:  3V7R Ki: min: 660, max: 660 (nM) from 2 assay(s)
IC50: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.6α = 90
b = 94.6β = 90
c = 130.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description