The Cambridge Structural Database (CSD) of Small Molecule Crystal Structures

Allen, Frank H.; Lipscomb, Karen J.; Battle,; Gary,

doi:10.1002/9783527618279.ch23

Cited by 3 publications

(4 citation statements)

References 38 publications

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“…The CSD was searched for compounds containing V 10 anion, the compounds were retrieved depending on the oxygen type Ob, Oc, Od, Oe, Of, and Og (30 structures found) . Con Quest software was used to search intermolecular contacts. The searches were restricted to entries with (a) error-free coordinate sets in CSD check procedures, (b) no crystallographic disorder, (c) no polymeric connections, (d) crystallographic R factors lower than 0.10, and (e) protons that were placed at their normalized position.…”

Section: Methodsmentioning

confidence: 99%

Crystallographic Statistical Study of Decavanadate Anion Based-Structures: Toward a Prediction of Noncovalent Interactions

Bošnjaković-Pavlović

Prévost

Biré

2011

Crystal Growth & Design

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We have retrieved from the Cambridge Structural Database (CSD), the Inorganic Crystal Structure Database (ICSD) and the Protein Data Bank (PDB) decavanadate based compounds, in order to find intermolecular interactions between decavanadate oxygen atom and different proton donor type (D = O, N, C). 63 different structures have been found containing decavanadate anion, leading to 2975 intermolecular contacts belonging to the 48 structures for which the hydrogen bonds have been localised. In a previous study, (Bosnjakovic-Pavlovic et al., Inorg. Chem., 2009) we have predicted the preferential noncovalent interactions with the different oxygen atoms of the decavanadate anion. These predictions are confirmed, in the present study. Noncovalent interactions are strongly different as a function of the oxygen atom type. The Ob, triply-linked, and Oc, double-linked oxygen atoms, for which the electrostatic potential in the vicinity have the lowest value, are mainly involved in the strong as O-H⋅⋅⋅O, N-H⋅⋅⋅O interactions, while the mono linked Of or Og are mainly involved in weakest noncovalent interactions such as C-H⋅⋅⋅O or cation interactions. Binding properties of decavanadate anion in biological systems are illustrated using PDB. Anion binding behaviour in small-molecule structures and in macromolecular structures is in good agreement. These results are important in the context of the various biological applications of the decavanadate such as, for example, inhibition of the Ca 2+ ATPase, myosin ATPase, and new development in insulin mimetic.

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Section: Methodsmentioning

confidence: 99%

Crystallographic Statistical Study of Decavanadate Anion Based-Structures: Toward a Prediction of Noncovalent Interactions

Bošnjaković-Pavlović

Prévost

Biré

2011

Crystal Growth & Design

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“…Typical numerical databases are Beilstein, , Gmelin, SpecInfo, KnowItAll, DETHERM, Cambridge Structural Database (CSD), − etc.…”

Section: Different Aspects Of Chemoinformaticsmentioning

confidence: 99%

“…Crystallographic structure databases, like the Inorganic Crystal Structure Database (ICSD), − Cambridge Structural Database (CSD), − and Protein Data Bank (PDB), , provide “real” 3D structures from X-ray crystallographic structure analyses.…”

Section: Different Aspects Of Chemoinformaticsmentioning

confidence: 99%

“…111 Another example of a structure database is the National Cancer Institute (NCI) database. 140 Crystallographic structure databases, like the Inorganic Crystal Structure Database (ICSD), [141][142][143] Cambridge Structural Database (CSD), [120][121][122] provide "real" 3D structures from X-ray crystallographic structure analyses. Patent databases including special structures are called Markush databases e.g.…”

Section: Chemicalmentioning

confidence: 99%

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Basic Overview of Chemoinformatics

Engel

2006

J. Chem. Inf. Model.

130

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There is no particular point in time that determines when chemoinformatics was founded or established. It slowly evolved from several, often quite humble beginnings. Scientists in various fields of chemistry struggled with the development of computer methods which allowed them to manage the enormous amount of chemical information and to find relationships between the structure and properties of a compound. During the 1960s some early developments appeared that led to a flurry of activities in the 1970s. This review provides a general overview of basic methods in the specific fields of chemoinformatics, from encoding chemical compounds, storing and searching data in databases, to generating and analyzing these data. In addition, the chief interconnecting points of chemoinformatics applications are highlighted including the contributions of Johann Gasteiger to this field.

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Chemical Information Systems and Databases

Engel¹,

Zaß²

2007

Comprehensive Medicinal Chemistry II

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The Cambridge Structural Database (CSD) of Small Molecule Crystal Structures

Cited by 3 publications

References 38 publications

Crystallographic Statistical Study of Decavanadate Anion Based-Structures: Toward a Prediction of Noncovalent Interactions

Crystallographic Statistical Study of Decavanadate Anion Based-Structures: Toward a Prediction of Noncovalent Interactions

Basic Overview of Chemoinformatics

Chemical Information Systems and Databases

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