Biology:Cambridge Structural Database

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Cambridge Structural Database
Database.png
Content
Description
Contact
Research centreCambridge Crystallographic Data Centre
Access
Data format.cif
Website
Web service URLwww.ccdc.cam.ac.uk/structures
Tools
Web applicationWebCSD
Computer software
  • 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.

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 995,907 100.0
# of different compounds 900,984 -
# of literature sources 2,004 -
Organic structures 431,037 43.5
Transition metal present 478,138 48.2
alkali or alkaline earth metal present 48,056 4.8
main group metal present 101,948 10.3
3D coordinates present 937,809 94.6
Error-free coordinates 926,422 98.81
Neutron studies 2,142 0.2
Powder diffraction studies 4,761 0.5
Low/high temp. studies 503,368 50.8
Absolute configuration determined 28,834 2.9
Disorder present in structure 256,019 25.8
Polymorphic structures 29,817 3.0
R-factor < 0.100 935,419 94.4
R-factor < 0.075 845,708 85.3
R-factor < 0.050 553,042 55.8
R-factor < 0.030 121,806 12.3
No. of atoms with 3D coordinates 85,791,623 -

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

1. 73,070 structures were reported in Inorg. Chem.
2. 62,072 structures were reported in Dalton & J. Chem. Soc., Dalton Trans.
3. 54,160 structures were reported in Organometallics
4. 48,967 structures were reported in J. Am. Chem. Soc.
5. 42,422 structures were reported in Acta Crystallogr. Sect. E
6. 32,610 structures were reported in Chem. Eur. J.
7. 29,790 structures were reported in J. Organomet. Chem.
8. 29,640 structures were reported in Angew. Chem. Int. Ed.
9. 28,682 structures were reported in Inorg. Chim. Acta
10. 28,351 structures were reported in Chem. Commun. & J. Chem. Soc.
11. 27,328 structures were reported in CSD Communications
12. 26,774 structures were reported in Acta Crystallogr. Sect. C
13. 26,734 structures were reported in Polyhedron
14. 24,045 structures were reported in Eur. J. Inorg. Chem.
15. 23,483 structures were reported in J. Org. Chem.
16. 22,286 structures were reported in Cryst. Growth Des.
17. 22,011 structures were reported in CrystEngComm
18. 15,985 structures were reported in Organic Letters
19. 15,424 structures were reported in Z. Anorg. Allg. Chem.
20. 14,864 structures were reported in Acta Crystallogr. Sect. B
21. 13,909 structures were reported in Tetrahedron 8,597 structures were reported as Private Communication to the CSD
22. 12,734 structures were reported in J. Mol. Struct.
23. 11,234 structures were reported in Tetrahedron Lett.
24. 9,150 structures were reported in Eur. J. Org. Chem.
25. 8,789 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.

Growth Trend of Structure in CSD from 1965 - 2018[11]
Number of published structures per year
Year # published Total
2018 53429 974,653
2017 55031 921,224
2016 54975 866,193
2015 53610 811,218
2014 50759 757,608
2013 48025 706,849
2012 45199 661,121
2011 43882 615,922
2010 41240 572,040
2009 40627 530,800
2008 36802 490,173
2007 36569 453,371
2006 34713 416,802
2005 31733 382,089
2004 27988 350,356
2003 26287 322,368
2002 24306 296,081
2001 21781 271,775
2000 19998 249,994
1999 18780 229,996
1998 17289 211,216
1997 15896 193,927
1996 15487 178,031
1995 13001 162,544
1994 12290 149,543
1993 12032 137,253
1992 10691 125,221
1991 9941 114,530
1990 8935 104,589
1989 7750 95,654
1988 7644 87,904
1987 7472 80,260
1986 6873 72,788
1985 6911 65,915
1984 6511 59,004
1983 5250 52,493
1982 5233 47,243
1981 4666 42,010
1980 4252 37,344
1979 3876 33,092
1978 3415 29,216
1977 3092 25,801
1976 2735 22,709
1975 2171 19,974
1974 2142 17,803
1973 1991 15,661
1972 1969 13,670
1971 1548 11,701
1970 1261 10,153
1969 1130 8,892
1968 975 7,762
1967 936 6,787
1966 683 5,851
1965 656 5,168
1923-1964 4512 4,512

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

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

  1. ↑ "CCDC CIF Depository Request Form". Cambridge Crystallographic Data Centre. http://www.ccdc.cam.ac.uk/Community/Requestastructure/Pages/DataRequest.aspx. 
  2. ↑ "CCDC Homepage". Cambridge Crystallographic Data Centre. http://www.ccdc.cam.ac.uk/. 
  3. ↑ "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. July 2009. doi:10.1007/s10822-009-9272-5. PMID 19421719. Bibcode: 2009JCAMD..23..391W. 
  4. ↑ "Announcement from the Chair, on behalf of Trustees" (in en). September 11, 2017. https://www.ccdc.cam.ac.uk/News/List/2017-09-11-ccdc-announcement/. 
  5. ↑ "The CCDC welcomes Jürgen Harter as CEO" (in en). June 11, 2018. https://www.ccdc.cam.ac.uk/News/List/2018-06-11-new-appointment/. 
  6. ↑ "CCDC opens US operations" (in en). October 30, 2013. https://www.ccdc.cam.ac.uk/News/List/post-25/. 
  7. ↑ "The Cambridge Crystallographic Data Centre Establishes U.S. Operations in New Partnership with Rutgers' Center for Integrative Proteomics Research". https://ored.rutgers.edu/content/cambridge-crystallographic-data-centre-establishes-us-operations-new-partnership-rutgers. 
  8. ↑ 8.0 8.1 "A crystallographic perspective on sharing data and knowledge". Journal of Computer-Aided Molecular Design 28 (10): 1015–22. October 2014. doi:10.1007/s10822-014-9780-9. PMID 25091065. Bibcode: 2014JCAMD..28.1015B. 
  9. ↑ "CSD Entries: Summary Statistics". Cambridge Crystallographic Data Centre. http://www.ccdc.cam.ac.uk/Lists/ResourceFileList/2014_stats_entries.pdf. 
  10. ↑ "CSD Entries: Summary Statistics". January 1, 2019. https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/bda77626c9db4747bc970a250820c3d2.pdf. 
  11. ↑ 11.0 11.1 "CSD Journal Statistics". January 1, 2019. https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/d22b66666a76428dad703137e9ad8e43.pdf. 
  12. ↑ "The Cambridge Structural Database in retrospect and prospect". Angewandte Chemie 53 (3): 662–71. January 2014. doi:10.1002/anie.201306438. PMID 24382699. 
  13. ↑ "Growth of the Cambridge Structural Database (CSD) since 1970.". CCDC. http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/CSD.aspx. 
  14. ↑ "CSD Statistics" (in en). https://www.ccdc.cam.ac.uk/CCDCStats/. 
  15. ↑ Robinson, Philip; Withers, Neil; Pink, Chris; Valsler, Ben. "The Cambridge Structural Database hits one million structures" (in en). https://www.chemistryworld.com/news/the-cambridge-structural-database-hits-one-million-structures/3010524.article. 
  16. ↑ "The Crystallographic Information File (CIF): a new standard archive file for crystallography". Acta Crystallographica A47 (6): 655–685. 1991. doi:10.1107/S010876739101067X. 
  17. ↑ Farrugia, Louis J. (1 August 1999). "WinGX suite for small-molecule single-crystal crystallography". Journal of Applied Crystallography 32 (4): 837–838. doi:10.1107/S0021889899006020. 
  18. ↑ "3D Printing: Easy as 1, 2, 3!" (in en). August 19, 2015. https://www.ccdc.cam.ac.uk/Community/blog/post-56/. 

External links



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