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Collections

A collection is a set of compounds reported in a published work having a citable DOI and the data covered under an open source license. COCONUT allows careful storage of the details of the source of the collections so as to ensure traceabitlity and authenticity of the data on the NPs.

COCONUT has NP data from 63 sources ranging from supplimentray resources to well curated databases. Despite the well curation efforts of these sources, the same compound from multiple source still has discrepancies that lead to confusion. To mitigate and resolve these discrepancies, COCONUT allows for live curation of compounds, organisms and sample locations from where the compounds were reported to be found and geo locations where these organisms were reported.

For a compound to be considered to be of natural origin, it should be reported to be found in an organism with a citable DOI. Veriety of ways are made available to the users to report synthetic compounds or suggest changes in data discrepancies of the NPs on the COCONUT DB.

New Collection Submission

Any collection directly submitted to COCONUT will be given its own DOI to enable citation of the collection.

To submit a new collection, please send your natural product data in CSV format to the COCONUT database by emailing info.coconut@uni-jena.de.

OR

To submit them directly on the COCONUT platform, follow the instructions here.

Data Distribution Disclaimer

We do not distribute the original data, as the rights belong to the original authors. You can download the original data directly from their website.

However, a curated version of the data available on COCONUT can be downloaded from the following link: https://coconut.naturalproducts.net/download. COCONUT make these downloads freely available to all under CC BY 4.0. This requires the users to provide citation upon using COCONUT curated data.

COCONUT was meticulously assembled from a range of public databases and primary sources, including:

S.NoDatabase nameEntries integrated in COCONUTLatest resource URL
1AfroCancer390Fidele Ntie-Kang, Justina Ngozi Nwodo, Akachukwu Ibezim, Conrad Veranso Simoben, Berin Karaman, Valery Fuh Ngwa, Wolfgang Sippl, Michael Umale Adikwu, and Luc Meva’a MbazeJournal of Chemical Information and Modeling 2014 54 (9), 2433-2450https://doi.org/10.1021/ci5003697
2AfroDB953Fidele Ntie-Kang ,Denis Zofou,Smith B. Babiaka,Rolande Meudom,Michael Scharfe,Lydia L. Lifongo,James A. Mbah,Luc Meva’a Mbaze,Wolfgang Sippl,Simon M. N. Efangehttps://doi.org/10.1371/journal.pone.0078085
3AfroMalariaDB265Onguéné, P.A., Ntie-Kang, F., Mbah, J.A. et al. The potential of anti-malarial compounds derived from African medicinal plants, part III: an in silico evaluation of drug metabolism and pharmacokinetics profiling. Org Med Chem Lett 4, 6 (2014). https://doi.org/10.1186/s13588-014-0006-x
4AnalytiCon Discovery NPs5,147Natural products are a sebset of AnalytiCon Discovery NPs https://ac-discovery.com/screening-libraries/
5BIOFACQUIM605Pilón-Jiménez, B.A.; Saldívar-González, F.I.; Díaz-Eufracio, B.I.; Medina-Franco, J.L. BIOFACQUIM: A Mexican Compound Database of Natural Products. Biomolecules 2019, 9, 31. https://doi.org/10.3390/biom9010031
6BitterDB685Ayana Dagan-Wiener, Antonella Di Pizio, Ido Nissim, Malkeet S Bahia, Nitzan Dubovski, Eitan Margulis, Masha Y Niv, BitterDB: taste ligands and receptors database in 2019, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1179–D1185, https://doi.org/10.1093/nar/gky974
7Carotenoids Database1,195Junko Yabuzaki, Carotenoids Database: structures, chemical fingerprints and distribution among organisms, Database, Volume 2017, 2017, bax004, https://doi.org/10.1093/database/bax004
8ChEBI NPs16,215Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, Gareth Owen, Steve Turner, Mark Williams, Christoph Steinbeck, The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D456–D463, https://doi.org/10.1093/nar/gks1146
9ChEMBL NPs1,910Anna Gaulton, Anne Hersey, Michał Nowotka, A. Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J. Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman, Anneli Karlsson, María Paula Magariños, John P. Overington, George Papadatos, Ines Smit, Andrew R. Leach, The ChEMBL database in 2017, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D945–D954, https://doi.org/10.1093/nar/gkw1074
10ChemSpider NPs9,740Harry E. Pence and Antony WilliamsJournal of Chemical Education 2010 87 (11), 1123-1124https://doi.org/10.1021/ed100697w
11CMAUP (cCollective molecular activities of useful plants)47,593Xian Zeng, Peng Zhang, Yali Wang, Chu Qin, Shangying Chen, Weidong He, Lin Tao, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen, CMAUP: a database of collective molecular activities of useful plants, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1118–D1127, https://doi.org/10.1093/nar/gky965
12ConMedNP3,111DOI https://doi.org/10.1039/C3RA43754J
13ETM (Ethiopian Traditional Medicine) DB1,798Bultum, L.E., Woyessa, A.M. & Lee, D. ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. BMC Complement Altern Med 19, 212 (2019). https://doi.org/10.1186/s12906-019-2634-1
14Exposome-explorer434Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S. Wishart, Augustin Scalbert, Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D979–D984, https://doi.org/10.1093/nar/gkw980
15FoodDB70,385Natural products are a sebset of FoodDB https://foodb.ca/
16GNPS (Global Natural Products Social Molecular Networking)11,103Wang, M., Carver, J., Phelan, V. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34, 828–837 (2016). https://doi.org/10.1038/nbt.3597
17HIM (Herbal Ingredients in-vivo Metabolism database)1,259Kang, H., Tang, K., Liu, Q. et al. HIM-herbal ingredients in-vivo metabolism database. J Cheminform 5, 28 (2013). https://doi.org/10.1186/1758-2946-5-28
18HIT (Herbal Ingredients Targets)530Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, Zhiwei Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research, Volume 39, Issue suppl_1, 1 January 2011, Pages D1055–D1059, https://doi.org/10.1093/nar/gkq1165
19Indofine Chemical Company46Natural products are a sebset of Indofine Chemical Company https://indofinechemical.com/
20InflamNat664Ruihan Zhang, Jing Lin, Yan Zou, Xing-Jie Zhang, and Wei-Lie XiaoJournal of Chemical Information and Modeling 2019 59 (1), 66-73DOI: 10.1021/acs.jcim.8b00560https://doi.org/10.1021/acs.jcim.8b00560
21InPACdb124Vetrivel et al., Bioinformation 4(2): 71-74 (2009)https://www.bioinformation.net/004/001500042009.htm
22InterBioScreen Ltd68,372Natural products are a sebset of InterBioScreen Ltd https://www.ibscreen.com/natural-compounds
23KNApSaCK48,241Kensuke Nakamura, Naoki Shimura, Yuuki Otabe, Aki Hirai-Morita, Yukiko Nakamura, Naoaki Ono, Md Altaf Ul-Amin, Shigehiko Kanaya, KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites, Plant and Cell Physiology, Volume 54, Issue 2, February 2013, Page e4, https://doi.org/10.1093/pcp/pcs186
24Lichen Database1,718Olivier-Jimenez, D., Chollet-Krugler, M., Rondeau, D. et al. A database of high-resolution MS/MS spectra for lichen metabolites. Sci Data 6, 294 (2019). https://doi.org/10.1038/s41597-019-0305-1
25Marine Natural Products14,220Gentile, D.; Patamia, V.; Scala, A.; Sciortino, M.T.; Piperno, A.; Rescifina, A. Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study. Mar. Drugs 2020, 18, 225. https://doi.org/10.3390/md18040225
26Mitishamba database1,095Derese, Solomon., Ndakala, Albert .,Rogo, Michael., Maynim, cholastica and Oyim, James (2015). Mitishamba database: a web based in silico database of natural products from Kenya plants. The 16th symposium of the natural products reseach network for eastern and central Africa (NAPRECA) 31st August to 3rd September 2015 Arusha, Tanzaniahttp://erepository.uonbi.ac.ke/handle/11295/92273
27NANPDB (Natural Products from Northern African Sources)7,482Fidele Ntie-Kang, Kiran K. Telukunta, Kersten Döring, Conrad V. Simoben, Aurélien F. A. Moumbock, Yvette I. Malange, Leonel E. Njume, Joseph N. Yong, Wolfgang Sippl, and Stefan GüntherJournal of Natural Products 2017 80 (7), 2067-2076DOI: 10.1021/acs.jnatprod.7b00283https://doi.org/10.1021/acs.jnatprod.7b00283
28NCI DTP data419Natural products are a sebset of NCI DTP data https://wiki.nci.nih.gov/display/NCIDTPdata/Compound+Sets
29NPACT1,572Manu Mangal, Parul Sagar, Harinder Singh, Gajendra P. S. Raghava, Subhash M. Agarwal, NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1124–D1129, https://doi.org/10.1093/nar/gks1047
30NPASS96,173Xian Zeng, Peng Zhang, Weidong He, Chu Qin, Shangying Chen, Lin Tao, Yali Wang, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen, NPASS: natural product activity and species source database for natural product research, discovery and tool development, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D1217–D1222, https://doi.org/10.1093/nar/gkx1026
31NPAtlas36,395Jeffrey A. van Santen, Grégoire Jacob, Amrit Leen Singh, Victor Aniebok, Marcy J. Balunas, Derek Bunsko, Fausto Carnevale Neto, Laia Castaño-Espriu, Chen Chang, Trevor N. Clark, Jessica L. Cleary Little, David A. Delgadillo, Pieter C. Dorrestein, Katherine R. Duncan, Joseph M. Egan, Melissa M. Galey, F.P. Jake Haeckl, Alex Hua, Alison H. Hughes, Dasha Iskakova, Aswad Khadilkar, Jung-Ho Lee, Sanghoon Lee, Nicole LeGrow, Dennis Y. Liu, Jocelyn M. Macho, Catherine S. McCaughey, Marnix H. Medema, Ram P. Neupane, Timothy J. O’Donnell, Jasmine S. Paula, Laura M. Sanchez, Anam F. Shaikh, Sylvia Soldatou, Barbara R. Terlouw, Tuan Anh Tran, Mercia Valentine, Justin J. J. van der Hooft, Duy A. Vo, Mingxun Wang, Darryl Wilson, Katherine E. Zink, and Roger G. LiningtonACS Central Science 2019 5 (11), 1824-1833DOI: 10.1021/acscentsci.9b00806https://doi.org/10.1021/acscentsci.9b00806
32NPCARE1,446Choi, H., Cho, S.Y., Pak, H.J. et al. NPCARE: database of natural products and fractional extracts for cancer regulation. J Cheminform 9, 2 (2017). https://doi.org/10.1186/s13321-016-0188-5
33NPEdia49,597Takeshi Tomiki, Tamio Saito, Masashi Ueki, Hideaki Konno, Takeo Asaoka, Ryuichiro Suzuki, Masakazu Uramoto, Hideaki Kakeya, Hiroyuki Osada, [Special Issue: Fact Databases and Freewares] RIKEN Natural Products Encyclopedia (RIKEN NPEdia),a Chemical Database of RIKEN Natural Products Depository (RIKEN NPDepo), Journal of Computer Aided Chemistry, 2006, Volume 7, Pages 157-162, Released on J-STAGE September 15, 2006, Online ISSN 1345-8647, https://doi.org/10.2751/jcac.7.157
34NuBBEDB2,215Pilon, A.C., Valli, M., Dametto, A.C. et al. NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. Sci Rep 7, 7215 (2017). https://doi.org/10.1038/s41598-017-07451-x
35p-ANAPL533Fidele Ntie-Kang ,Pascal Amoa Onguéné ,Ghislain W. Fotso,Kerstin Andrae-Marobela ,Merhatibeb Bezabih,Jean Claude Ndom,Bonaventure T. Ngadjui,Abiodun O. Ogundaini,Berhanu M. Abegaz,Luc Mbaze Meva’a Published: March 5, 2014https://doi.org/10.1371/journal.pone.0090655
36Phenol-explorer742Joseph A. Rothwell, Jara Perez-Jimenez, Vanessa Neveu, Alexander Medina-Remón, Nouha M'Hiri, Paula García-Lobato, Claudine Manach, Craig Knox, Roman Eisner, David S. Wishart, Augustin Scalbert, Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content, Database, Volume 2013, 2013, bat070, https://doi.org/10.1093/database/bat070
37PubChem NPs3,533Natural products are a sebset of PubChem NPs https://pubchem.ncbi.nlm.nih.gov/substance/251960601
38ReSpect4,854Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki, Masami Yokota Hirai, Kazuki Saito,RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database,Phytochemistry,Volume 82,2012,Pages 38-45,ISSN 0031-9422,https://doi.org/10.1016/j.phytochem.2012.07.007.
39SANCDB995Hatherley, R., Brown, D.K., Musyoka, T.M. et al. SANCDB: a South African natural compound database. J Cheminform 7, 29 (2015). https://doi.org/10.1186/s13321-015-0080-8
40Seaweed Metabolite Database (SWMD)1,075Davis & Vasanthi, Bioinformation 5(8): 361-364 (2011)https://www.bioinformation.net/005/007900052011.htm
41Specs Natural Products744Natural products are a sebset of Specs Natural Products https://www.specs.net/index.php
42Spektraris NMR248Justin T. Fischedick, Sean R. Johnson, Raymond E.B. Ketchum, Rodney B. Croteau, B. Markus Lange,NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification – Taxane diterpenoids from Taxus×media cell suspension cultures as a case study,Phytochemistry,Volume 113,2015,Pages 87-95,ISSN 0031-9422,https://doi.org/10.1016/j.phytochem.2014.11.020.
43StreptomeDB6,522Aurélien F A Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A Kirchner, Bakoh Ndingkokhar, Boris D Bekono, Conrad V Simoben, Smith B Babiaka, Yvette I Malange, Florian Sauter, Paul Zierep, Fidele Ntie-Kang, Stefan Günther, StreptomeDB 3.0: an updated compendium of streptomycetes natural products, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D600–D604, https://doi.org/10.1093/nar/gkaa868
44Super Natural II325,149Priyanka Banerjee, Jevgeni Erehman, Björn-Oliver Gohlke, Thomas Wilhelm, Robert Preissner, Mathias Dunkel, Super Natural II—a database of natural products, Nucleic Acids Research, Volume 43, Issue D1, 28 January 2015, Pages D935–D939, https://doi.org/10.1093/nar/gku886
45TCMDB@Taiwan (Traditional Chinese Medicine database)58,401Calvin Yu-Chian Chen Published: January 6, 2011https://doi.org/10.1371/journal.pone.0015939
46TCMID (Traditional Chinese Medicine Integrated Database)32,038Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D1089-95. doi: 10.1093/nar/gks1100. Epub 2012 Nov 29. PMID: 23203875; PMCID: PMC3531123.
47TIPdb (database of Taiwan indigenous plants)8,838Chun-Wei Tung, Ying-Chi Lin, Hsun-Shuo Chang, Chia-Chi Wang, Ih-Sheng Chen, Jhao-Liang Jheng, Jih-Heng Li, TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants, Database, Volume 2014, 2014, bau055, https://doi.org/10.1093/database/bau055
48TPPT (Toxic Plants–PhytoToxins)1,561Barbara F. Günthardt, Juliane Hollender, Konrad Hungerbühler, Martin Scheringer, and Thomas D. BucheliJournal of Agricultural and Food Chemistry 2018 66 (29), 7577-7588DOI: 10.1021/acs.jafc.8b01639https://pubs.acs.org/doi/10.1021/acs.jafc.8b01639
49UEFS (Natural Products Databse of the UEFS)503Natural products are a sebset of UEFS (Natural Products Databse of the UEFS) https://zinc12.docking.org/catalogs/uefsnp
50UNPD (Universal Natural Products Database)213,210Jiangyong Gu,Yuanshen Gui,Lirong Chen ,Gu Yuan,Hui-Zhe Lu,Xiaojie Xu Published: April 25, 2013https://doi.org/10.1371/journal.pone.0062839
51VietHerb5,150Thanh-Hoang Nguyen-Vo, Tri Le, Duy Pham, Tri Nguyen, Phuc Le, An Nguyen, Thanh Nguyen, Thien-Ngan Nguyen, Vu Nguyen, Hai Do, Khang Trinh, Hai Trong Duong, and Ly LeJournal of Chemical Information and Modeling 2019 59 (1), 1-9DOI: 10.1021/acs.jcim.8b00399https://pubs.acs.org/doi/10.1021/acs.jcim.8b00399
52ZINC NP85,201Teague Sterling and John J. IrwinJournal of Chemical Information and Modeling 2015 55 (11), 2324-2337DOI: 10.1021/acs.jcim.5b00559https://doi.org/10.1021/acs.jcim.5b00559
53CyanoMetNP2,113Jones MR, Pinto E, Torres MA, Dörr F, Mazur-Marzec H, Szubert K, Tartaglione L, Dell'Aversano C, Miles CO, Beach DG, McCarron P, Sivonen K, Fewer DP, Jokela J, Janssen EM. CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria. Water Res. 2021 May 15;196:117017. doi: 10.1016/j.watres.2021.117017. Epub 2021 Mar 8. PMID: 33765498.
54DrugBankNP9,283Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2017 Nov 8. doi: 10.1093/nar/gkx1037.
55Australian natural products21,591Saubern, Simon; Shmaylov, Alex; Locock, Katherine; McGilvery, Don; Collins, David (2023): Australian Natural Products dataset. v5. CSIRO. Data Collection. https://doi.org/10.25919/v8wq-mr81
56EMNPD6,145Xu, HQ., Xiao, H., Bu, JH. et al. EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances. J Cheminform 15, 115 (2023). https://doi.org/10.1186/s13321-023-00779-9
57ANPDB7,4821) Pharmacoinformatic investigation of medicinal plants from East Africa Conrad V. Simoben, Ammar Qaseem, Aurélien F. A. Moumbock, Kiran K. Telukunta, Stefan Günther, Wolfgang Sippl, and Fidele Ntie-KangMolecular Informatics 2020DOI: 10.1002/minf.202000163 https://doi.org/10.1002/minf.2020001632) NANPDB: A Resource for Natural Products from Northern African SourcesFidele Ntie-Kang, Kiran K. Telukunta, Kersten Döring, Conrad V. Simoben, Aurélien F. A. Moumbock, Yvette I. Malange, Leonel E. Njume, Joseph N. Yong, Wolfgang Sippl, and Stefan GüntherJournal of Natural Products 2017DOI: 10.1021/acs.jnatprod.7b00283https://pubs.acs.org/doi/10.1021/acs.jnatprod.7b00283
58Phyto4Health3,175Nikita Ionov, Dmitry Druzhilovskiy, Dmitry Filimonov, and Vladimir PoroikovJournal of Chemical Information and Modeling 2023 63 (7), 1847-1851DOI: 10.1021/acs.jcim.2c01567https://pubs.acs.org/doi/10.1021/acs.jcim.2c01567
59Piella DB65Natural products are a sebset of Piella DB https://micro.biol.ethz.ch/research/piel.html
60Watermelon1,526Natural products are a sebset of Watermelon https://watermelon.naturalproducts.net/
61Latin America dataset12,959Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel). 2023 Sep 30;16(10):1388. doi: 10.3390/ph16101388. PMID: 37895859; PMCID: PMC10609821.
62CMNPD31,561Chuanyu Lyu, Tong Chen, Bo Qiang, Ningfeng Liu, Heyu Wang, Liangren Zhang, Zhenming Liu, CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D509–D515, https://doi.org/10.1093/nar/gkaa763
63Supernatural31,203,509Natural products are a sebset of Supernatural3 https://academic.oup.com/nar/article/51/D1/D654/6833249