Cambridge Structural Database

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Cambridge Structural Database
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Content
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Contact
Research centerCambridge Crystallographic Data Centre
Access
Data format.cif
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Web service URLwww.ccdc.cam.ac.uk/structures
Tools
WebWebCSD
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  • CSD System
  • CSD (the database)
  • ConQuest
  • Mercury
  • IsoStar
  • Mogul
  • GOLD
  • CSD-CrossMiner

The Cambridge Structural Database (CSD) is both a repository and a validated and curated resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal-organic and organometallic molecules. The specific entries are complementary to the other crystallographic databases such as the Protein Data Bank (PDB), Inorganic Crystal Structure Database and International Centre for Diffraction Data. The data, typically obtained by X-ray crystallography and less frequently by electron diffraction or neutron diffraction, and submitted by crystallographers and chemists from around the world, are freely accessible (as deposited by authors) on the Internet via the CSD's parent organization's website (CCDC, Repository[1]). The CSD is overseen by the not-for-profit incorporated company called the Cambridge Crystallographic Data Centre, CCDC.

File:The inside of the CCDC headquarters Cambridge, UK.jpg
The inside of the CCDC headquarters Cambridge, UK

The CSD is a widely used repository for small-molecule organic and metal-organic crystal structures for scientists. Structures deposited with Cambridge Crystallographic Data Centre (CCDC) are publicly available for download at the point of publication or at consent from the depositor. They are also scientifically enriched and included in the database used by software offered by the centre. Targeted subsets of the CSD are also freely available to support teaching and other activities.[2]

History

The CCDC grew out of the activities of the crystallography group led by Olga Kennard OBE FRS in the Department of Organic, Inorganic and Theoretical Chemistry of the University of Cambridge. From 1965, the group began to collect published bibliographic, chemical and crystal structure data for all small molecules studied by X-ray or neutron diffraction. With the rapid developments in computing taking place at this time, this collection was encoded in electronic form and became known as the Cambridge Structural Database (CSD).

The CSD was one of the first numerical scientific databases to begin operations anywhere in the world, and received academic grants from the UK Office for Scientific and Technical Information and then from the UK Science and Engineering Research Council. These funds, together with subventions from National Affiliated Centres, enabled the development of the CSD and its associated software during the 1970s and 1980s. The first releases of the CSD System to the United States, Italy and Japan occurred in the early 1970s. By the early 1980s the CSD System was being distributed in more than 30 countries. As of 2014, the CSD System was distributed to academics in 70 countries.

During the 1980s, interest in the CSD System from pharmaceutical and agrochemicals companies increased significantly. This led to the establishment of the Cambridge Crystallographic Data Centre (CCDC) as an independent company in 1987, with the legal status of a non-profit charitable institution, and with its operations overseen by an international board of governors. The CCDC moved into purpose-built premises on the site of the University Department of Chemistry in 1992.

Kennard retired as Director in 1997 and was succeeded by David Hartley (1997-2002) and Frank Allen (2002-2008). Colin Groom was appointed as executive director from 1 October 2008[3] to September 2017.[4] And most recently, Juergen Harter was appointed CEO in June 2018.[5]

CCDC software products diversified to the use of crystallographic data in applications in the life sciences and crystallography. Much of this software development and marketing is carried out by CCDC Software Limited (founded in 1998), a wholly owned subsidiary which covenants all of its profits back to the CCDC.

Although the CCDC is a self-administering organization, it retains close links with the University of Cambridge, and is a University Partner Institution that is qualified to train postgraduate students for higher degrees (PhD, MPhil).

The CCDC established US applications and support operations in the US in October 2013,[6][7] initially at Rutgers, the State University of New Jersey, where it is co-located with the RCSB Protein Data Bank

Contents

One Millionth Structure Added to CSD
One Millionth Structure Added to CSD, CSD ID: XOPCAJ

The CSD is updated with about 50,000 new structures each year,[8] and with improvements to existing entries. Entries (structures) in the repository are released for public access as soon as the corresponding entry has appeared in the peer-reviewed scientific literature. Meanwhile, data can also be deposited and published directly through the CSD without an accompanying scientific article as what is known as a CSD Communication.

Periodically, general statistics about the breadth of CSD holdings are reported, for example the January 2014 report.[9] As of January 2019, the summary statistics are as follows:[10]

Query structures % of CSD
Total # of structures Script error: No such module "Number table sorting". 100.0
# of different compounds Script error: No such module "Number table sorting". -
# of literature sources Script error: No such module "Number table sorting". -
Organic structures Script error: No such module "Number table sorting". 43.5
Transition metal present Script error: No such module "Number table sorting". 48.2
alkali or alkaline earth metal present Script error: No such module "Number table sorting". 4.8
main group metal present Script error: No such module "Number table sorting". 10.3
3D coordinates present Script error: No such module "Number table sorting". 94.6
Error-free coordinates Script error: No such module "Number table sorting". 98.81
Neutron studies Script error: No such module "Number table sorting". 0.2
Powder diffraction studies Script error: No such module "Number table sorting". 0.5
Low/high temp. studies Script error: No such module "Number table sorting". 50.8
Absolute configuration determined Script error: No such module "Number table sorting". 2.9
Disorder present in structure Script error: No such module "Number table sorting". 25.8
Polymorphic structures Script error: No such module "Number table sorting". 3.0
R-factor < 0.100 Script error: No such module "Number table sorting". 94.4
R-factor < 0.075 Script error: No such module "Number table sorting". 85.3
R-factor < 0.050 Script error: No such module "Number table sorting". 55.8
R-factor < 0.030 Script error: No such module "Number table sorting". 12.3
No. of atoms with 3D coordinates Script error: No such module "Number table sorting". -

As of January 2019, the top 25 scientific journals in terms of publication of structures in the CSD repository were:[11]

1. Script error: No such module "Number table sorting". structures were reported in Inorg. Chem.
2. Script error: No such module "Number table sorting". structures were reported in Dalton & J. Chem. Soc., Dalton Trans.
3. Script error: No such module "Number table sorting". structures were reported in Organometallics
4. Script error: No such module "Number table sorting". structures were reported in J. Am. Chem. Soc.
5. Script error: No such module "Number table sorting". structures were reported in Acta Crystallogr. Sect. E
6. Script error: No such module "Number table sorting". structures were reported in Chem. Eur. J.
7. Script error: No such module "Number table sorting". structures were reported in J. Organomet. Chem.
8. Script error: No such module "Number table sorting". structures were reported in Angew. Chem. Int. Ed.
9. Script error: No such module "Number table sorting". structures were reported in Inorg. Chim. Acta
10. Script error: No such module "Number table sorting". structures were reported in Chem. Commun. & J. Chem. Soc.
11. Script error: No such module "Number table sorting". structures were reported in CSD Communications
12. Script error: No such module "Number table sorting". structures were reported in Acta Crystallogr. Sect. C
13. Script error: No such module "Number table sorting". structures were reported in Polyhedron
14. Script error: No such module "Number table sorting". structures were reported in Eur. J. Inorg. Chem.
15. Script error: No such module "Number table sorting". structures were reported in J. Org. Chem.
16. Script error: No such module "Number table sorting". structures were reported in Cryst. Growth Des.
17. Script error: No such module "Number table sorting". structures were reported in CrystEngComm
18. Script error: No such module "Number table sorting". structures were reported in Organic Letters
19. Script error: No such module "Number table sorting". structures were reported in Z. Anorg. Allg. Chem.
20. Script error: No such module "Number table sorting". structures were reported in Acta Crystallogr. Sect. B
21. Script error: No such module "Number table sorting". structures were reported in Tetrahedron Script error: No such module "Number table sorting". structures were reported as Private Communication to the CSD
22. Script error: No such module "Number table sorting". structures were reported in J. Mol. Struct.
23. Script error: No such module "Number table sorting". structures were reported in Tetrahedron Lett.
24. Script error: No such module "Number table sorting". structures were reported in Eur. J. Org. Chem.
25. Script error: No such module "Number table sorting". structures were reported in New Journal of Chemistry

These 25 journals account for 704,541 of the 996,193 or 70.7% of the structures in the CSD.

These data show that most structures are determined by X-ray diffraction, with less than 1% of structures being determined by neutron diffraction or powder diffraction. The number of error-free coordinates were taken as a percentage of structures for which 3D coordinates are present in the CSD.

The significance of the structure factor files, mentioned above, is that, for CSD structures determined by X-ray diffraction that have a structure file, a crystallographer can verify the interpretation of the observed measurements.

Growth trend

Historically, the number of structures in the CSD has grown at an approximately exponential rate passing the 25,000 structures milestone in 1977, the 50,000 structures milestone in 1983, the 125,000 structures milestone in 1992, the 250,000 structures milestone in 2001, the 500,000 structures milestone in 2009,[12][13][14] and the 1,000,000 structures milestone on June 8, 2019.[15] The one millionth structure added to CSD is the crystal structure of 1-(7,9-diacetyl-11-methyl-6H-azepino[1,2-a]indol-6-yl)propan-2-one.

File:Growth Trend of Structure in CSD.svg
Growth Trend of Structure in CSD from 1965 - 2018[11]
Number of published structures per year
Year # published Total
2018 53429 Script error: No such module "Number table sorting".
2017 55031 Script error: No such module "Number table sorting".
2016 54975 Script error: No such module "Number table sorting".
2015 53610 Script error: No such module "Number table sorting".
2014 50759 Script error: No such module "Number table sorting".
2013 48025 Script error: No such module "Number table sorting".
2012 45199 Script error: No such module "Number table sorting".
2011 43882 Script error: No such module "Number table sorting".
2010 41240 Script error: No such module "Number table sorting".
2009 40627 Script error: No such module "Number table sorting".
2008 36802 Script error: No such module "Number table sorting".
2007 36569 Script error: No such module "Number table sorting".
2006 34713 Script error: No such module "Number table sorting".
2005 31733 Script error: No such module "Number table sorting".
2004 27988 Script error: No such module "Number table sorting".
2003 26287 Script error: No such module "Number table sorting".
2002 24306 Script error: No such module "Number table sorting".
2001 21781 Script error: No such module "Number table sorting".
2000 19998 Script error: No such module "Number table sorting".
1999 18780 Script error: No such module "Number table sorting".
1998 17289 Script error: No such module "Number table sorting".
1997 15896 Script error: No such module "Number table sorting".
1996 15487 Script error: No such module "Number table sorting".
1995 13001 Script error: No such module "Number table sorting".
1994 12290 Script error: No such module "Number table sorting".
1993 12032 Script error: No such module "Number table sorting".
1992 10691 Script error: No such module "Number table sorting".
1991 9941 Script error: No such module "Number table sorting".
1990 8935 Script error: No such module "Number table sorting".
1989 7750 Script error: No such module "Number table sorting".
1988 7644 Script error: No such module "Number table sorting".
1987 7472 Script error: No such module "Number table sorting".
1986 6873 Script error: No such module "Number table sorting".
1985 6911 Script error: No such module "Number table sorting".
1984 6511 Script error: No such module "Number table sorting".
1983 5250 Script error: No such module "Number table sorting".
1982 5233 Script error: No such module "Number table sorting".
1981 4666 Script error: No such module "Number table sorting".
1980 4252 Script error: No such module "Number table sorting".
1979 3876 Script error: No such module "Number table sorting".
1978 3415 Script error: No such module "Number table sorting".
1977 3092 Script error: No such module "Number table sorting".
1976 2735 Script error: No such module "Number table sorting".
1975 2171 Script error: No such module "Number table sorting".
1974 2142 Script error: No such module "Number table sorting".
1973 1991 Script error: No such module "Number table sorting".
1972 1969 Script error: No such module "Number table sorting".
1971 1548 Script error: No such module "Number table sorting".
1970 1261 Script error: No such module "Number table sorting".
1969 1130 Script error: No such module "Number table sorting".
1968 975 Script error: No such module "Number table sorting".
1967 936 Script error: No such module "Number table sorting".
1966 683 Script error: No such module "Number table sorting".
1965 656 Script error: No such module "Number table sorting".
1923-1964 4512 Script error: No such module "Number table sorting".

Note: data for 1923-1964 are aggregated together in the last line of the table.

File format

3D printed model of Benzoic Acid
3D printed model of Benzoic Acid, taken from a crystal structure determination, created using coordinates from the Cambridge Structural Database, and via the CCDC program Mercury. The top model shows a single molecule of benzoic acid. The bottom model shows a hydrogen-bonded dimer.

The primary file format for CSD structure deposition, adopted around 1991, is the "Crystallographic Information file" format, CIF.[16]

The deposited CSD files can be downloaded in the CIF format. The validated and curated CSD files can be exported in a wide range of formats, including CIF, MOL, Mol2, PDB, SHELX and XMol, using tools in the CSD System.

The CCDC uses two different codes to distinguish between the deposited dataset and the curated CSD entry. For example, one specific ‘CSD Communication’ of an organic molecule was deposited with the CCDC and assigned the deposition number 'CCDC-991327.' This allows free public access to the data as deposited. From the deposited data, selected information is extracted to prepare the validated and curated CSD entry which was assigned the refcode 'MITGUT'. As a part of the curation process, CCDC also applies an algorithm, DeCIFer, to help the editors assign chemistry to structures when those representations (e.g. bond types and charge assignments etc.) are missing from the original CIF files submitted.[8] The validated and curated entry is included in the CSD System and WebCSD distributions, with availability restricted to those making appropriate contributions.

Viewing the data

File:XURZAN.jpg
3D printed model of 1-methyl-2,3,4,5-tetrakis((trimethylsilyl)ethynyl)-1H-pyrrole structure. CSD Identifier: XURZAN

Each data set in CSD can be openly viewed and retrieved using the free Access Structure service. Through this web-browser based service, users can view the data set in 2D and 3D, obtain some basic information about the structure, and download the deposited data set. More advanced search functions and curated information are available through the subscription based CSD system.

Besides using the CSD system, the structure files may be viewed using one of several open source computer programs such as Jmol. Some other free, but not open source programs include MDL Chime, Pymol, UCSF Chimera, Rasmol, WINGX,[17] the CCDC provides a free version of its visualization program Mercury.

Starting from 2015, Mercury from CCDC also provides the functionality to generate 3D print ready file from structures in CSD.[18]

See also

References

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  1. ^ Page Module:Citation/CS1/styles.css has no content."CCDC CIF Depository Request Form". Cambridge Crystallographic Data Centre. Retrieved 2014-09-16.
  2. ^ Page Module:Citation/CS1/styles.css has no content."CCDC Homepage". Cambridge Crystallographic Data Centre. Retrieved 2014-09-16.
  3. ^ Page Module:Citation/CS1/styles.css has no content.Groom C, Allen F (July 2009). "CCDC well groomed: an interview with Colin Groom, Executive Director, Cambridge Crystallographic Data Centre, and Frank Allen, Emeritus Fellow". Journal of Computer-Aided Molecular Design. 23 (7): 391–4. Bibcode:2009JCAMD..23..391W. doi:10.1007/s10822-009-9272-5. PMID 19421719.
  4. ^ Page Module:Citation/CS1/styles.css has no content."Announcement from the Chair, on behalf of Trustees". The Cambridge Crystallographic Data Centre. September 11, 2017. Retrieved 2019-05-15.
  5. ^ Page Module:Citation/CS1/styles.css has no content."The CCDC welcomes Jürgen Harter as CEO". The Cambridge Crystallographic Data Centre (CCDC). June 11, 2018. Retrieved 2019-05-15.
  6. ^ Page Module:Citation/CS1/styles.css has no content."CCDC opens US operations". The Cambridge Crystallographic Data Centre (CCDC). October 30, 2013. Retrieved 2019-05-15.
  7. ^ Page Module:Citation/CS1/styles.css has no content."The Cambridge Crystallographic Data Centre Establishes U.S. Operations in New Partnership with Rutgers' Center for Integrative Proteomics Research". Rutgers Office of Research and Economic Development. Retrieved May 15, 2019.
  8. ^ a b Page Module:Citation/CS1/styles.css has no content.Bruno IJ, Groom CR (October 2014). "A crystallographic perspective on sharing data and knowledge". Journal of Computer-Aided Molecular Design. 28 (10): 1015–22. Bibcode:2014JCAMD..28.1015B. doi:10.1007/s10822-014-9780-9. PMC 4196029. PMID 25091065.
  9. ^ Page Module:Citation/CS1/styles.css has no content."CSD Entries: Summary Statistics" (PDF). Cambridge Crystallographic Data Centre. Archived from the original (PDF) on 2014-06-11. Retrieved 2014-09-16.
  10. ^ Page Module:Citation/CS1/styles.css has no content."CSD Entries: Summary Statistics" (PDF). Cambridge Structural Database. January 1, 2019. Retrieved May 15, 2019.
  11. ^ a b Page Module:Citation/CS1/styles.css has no content."CSD Journal Statistics" (PDF). Cambridge Structural Database. January 1, 2019. Retrieved May 16, 2019.
  12. ^ Page Module:Citation/CS1/styles.css has no content.Groom CR, Allen FH (January 2014). "The Cambridge Structural Database in retrospect and prospect". Angewandte Chemie. 53 (3): 662–71. doi:10.1002/anie.201306438. PMID 24382699.
  13. ^ Page Module:Citation/CS1/styles.css has no content."Growth of the Cambridge Structural Database (CSD) since 1970". CCDC. Retrieved 2014-09-16.
  14. ^ Page Module:Citation/CS1/styles.css has no content."CSD Statistics". The Cambridge Crystallographic Data Centre (CCDC). Retrieved 2019-05-17.
  15. ^ Page Module:Citation/CS1/styles.css has no content.Robinson, Philip; Withers, Neil; Pink, Chris; Valsler, Ben. "The Cambridge Structural Database hits one million structures". Chemistry World. Retrieved 2019-06-07.
  16. ^ Page Module:Citation/CS1/styles.css has no content.Hall SR, Allen FH, Brown ID (1991). "The Crystallographic Information File (CIF): a new standard archive file for crystallography". Acta Crystallographica. A47 (6): 655–685. doi:10.1107/S010876739101067X.
  17. ^ Page Module:Citation/CS1/styles.css has no content.Farrugia LJ (1 August 1999). "WinGX suite for small-molecule single-crystal crystallography". Journal of Applied Crystallography. 32 (4): 837–838. doi:10.1107/S0021889899006020.
  18. ^ Page Module:Citation/CS1/styles.css has no content."3D Printing: Easy as 1, 2, 3!". The Cambridge Crystallographic Data Centre (CCDC). August 19, 2015. Retrieved 2019-05-18.


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