scholarly journals The impact of the Cambridge Structural Database and the small molecule crystal structures it contains: a bibliographic and literature study

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7233-7241 ◽  
Author(s):  
Peter Willett ◽  
Jason C. Cole ◽  
Ian J. Bruno
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Cambridge Structural Database ◽  
Literature Study ◽  
Structural Database ◽  
The Impact

A bibliographic and literature-based analysis of the impact of the Cambridge Structural Database (CSD) and the papers associated with crystal structures in the CSD has been undertaken.

scholarly journals The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

2017 ◽  
Vol 73 (3) ◽  
pp. 240-245 ◽  
Author(s):  
Colin R. Groom ◽  
Jason C. Cole
Keyword(s):  
Drug Discovery ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structural Chemistry ◽  
Cambridge Structural Database ◽  
Complement Protein ◽  
Ligand Discovery ◽  
Structural Database ◽  
Core Part

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2002 ◽  
Vol 58 (3) ◽  
pp. 380-388 ◽  
Author(s):  
Frank H. Allen
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Data ◽  
Crystal Structure Data ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
Chemical Information ◽  
Structural Database ◽  
Statistical Survey

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

First global analysis of the GSK database of small molecule crystal structures

CrystEngComm ◽  
2021 ◽  
Author(s):  
Leen N. Kalash ◽  
Jason C. Cole ◽  
Royston C. B. Copley ◽  
Colin M. Edge ◽  
Alexandru A. Moldovan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Small Molecule ◽  
Global Analysis ◽  
Structural Features ◽  
Cambridge Structural Database ◽  
Structure Database ◽  
Structural Database ◽  
Crystal Structure Database

Analysis of the molecular and structural features of the GSK crystal structure database and Cambridge Structural Database leads to improved reliability in hydrogen bond propensity models for pharmaceutical polymorphs.

scholarly journals The development and use of a crystallographic database

2016 ◽  
Vol 72 (2) ◽  
pp. 167-168 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Organometallic Compounds ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Individual Crystal ◽  
Data Source ◽  
Structural Database

To scientists working with small-molecule or organometallic compounds, the Cambridge Structural Database constitutes an extremely important tool for reference to individual crystal structures and as a data source for statistical investigations. The article by Groomet al.[(2016),Acta Cryst.B72, 171–179] provides updated information on the use, development and future of this database.

scholarly journals Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis. Addendum

2017 ◽  
Vol 73 (12) ◽  
pp. 1029-1029
Author(s):  
Jason C. Cole ◽  
Ilenia Giangreco ◽  
Colin R. Groom
Keyword(s):  
Protein Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Refinement ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Protein Structure Refinement ◽  
Structure Solution ◽  
Structural Database

An addendum to theIntroductionof Coleet al.[(2017),Acta Cryst.D73, 234–239] is made to recognize the work of Bricogne, Smart and others in the development of methods to make use of Cambridge Structural Database data in protein structure solution.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Rings ◽  
Structural Database

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings have been studied by analyzing crystal structures in the Cambridge Structural Database and performing quantum chemical calculations.

GRX: a program to search the CSD for functional group exchanges

2005 ◽  
Vol 38 (4) ◽  
pp. 694-696 ◽  
Author(s):  
Jacco van de Streek ◽  
Sam Motherwell
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Functional Group ◽  
Cambridge Structural Database ◽  
Structural Database

In order to establish the effect of exchanging one functional group by another on the crystal structure, one would like to be able to search the Cambridge Structural Database for all pairs of crystal structures where this substitution has been made. A program calledGRX(group exchange) was written for that purpose.

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