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PDBsum entry 1c0r
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PDB id:
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Antibiotic
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Title:
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Complex of vancomycin with d-lactic acid
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Structure:
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Vancomycin. Chain: a, b. Engineered: yes
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Source:
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Amycolatopsis orientalis. Organism_taxid: 31958
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Resolution:
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1.00Å
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R-factor:
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0.114
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R-free:
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0.142
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Authors:
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P.J.Loll,J.Kaplan,B.Selinsky,P.H.Axelsen
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Key ref:
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P.J.Loll
et al.
(1999).
Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding.
J Med Chem,
42,
4714-4719.
PubMed id:
DOI:
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Date:
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20-Jul-99
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Release date:
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30-Jul-99
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Headers
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References
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DOI no:
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J Med Chem
42:4714-4719
(1999)
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PubMed id:
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Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding.
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P.J.Loll,
J.Kaplan,
B.S.Selinsky,
P.H.Axelsen.
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ABSTRACT
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Bacterial resistance to vancomycin has been attributed to the loss of an
intermolecular hydrogen bond between vancomycin and its peptidoglycan target
when cell wall biosynthesis proceeds via depsipeptide intermediates rather than
the usual polypeptide intermediates. To investigate the relative importance of
this hydrogen bond to vancomycin binding, we have determined crystal structures
at 1.0 A resolution for the vancomycin complexes with three ligands that mimic
peptides and depsipeptides found in vancomycin-sensitive and
vancomycin-resistant bacteria: N-acetylglycine, D-lactic acid, and
2-acetoxy-D-propanoic acid. These, in conjunction with structures that have been
reported previously, indicate higher-affinity ligands elicit a structural change
in the drug not seen with these low-affinity ligands. They also enable us to
define a minimal set of drug-ligand interactions necessary to confer
higher-affinity binding on a ligand. Most importantly, these structures point to
factors in addition to the loss of an intermolecular hydrogen bond that must be
invoked to explain the weaker affinity of vancomycin for depsipeptide ligands.
These factors are important considerations for the design of vancomycin
analogues to overcome vancomycin resistance.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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P.J.Loll,
A.Derhovanessian,
M.V.Shapovalov,
J.Kaplan,
L.Yang,
and
P.H.Axelsen
(2009).
Vancomycin forms ligand-mediated supramolecular complexes.
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J Mol Biol,
385,
200-211.
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M.E.Piyasena,
L.J.Real,
R.A.Diamond,
H.H.Xu,
and
F.A.Gomez
(2008).
Magnetic microsphere-based methods to study the interaction of teicoplanin with peptides and bacteria.
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Anal Bioanal Chem,
392,
877-886.
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X.Li,
A.V.Volkov,
K.Szalewicz,
and
P.Coppens
(2006).
Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials.
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Acta Crystallogr D Biol Crystallogr,
62,
639-647.
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N.E.Allen,
and
T.I.Nicas
(2003).
Mechanism of action of oritavancin and related glycopeptide antibiotics.
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FEMS Microbiol Rev,
26,
511-532.
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B.M.Grail,
and
J.W.Payne
(2002).
Conformational analysis of bacterial cell wall peptides indicates how particular conformations have influenced the evolution of penicillin-binding proteins, beta-lactam antibiotics and antibiotic resistance mechanisms.
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J Mol Recognit,
15,
113-125.
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P.J.Loll,
and
P.H.Axelsen
(2000).
The structural biology of molecular recognition by vancomycin.
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Annu Rev Biophys Biomol Struct,
29,
265-289.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
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