DOI: 10.5281/zenodo.13692394
title: COCONUT 2.0 - Complete database

description: COCONUT Release Notes:



Curated approx 2500 duplicate organism entries (reassigned molecules and audit logged)

Removed duplicate entries in the molecules table (reassigned the associations to the retained entries)

Recalculated counts and annotation scores

Citations mapped for more molecules


COCONUT (Collection of Open Natural Products) Online

COlleCtion of Open NatUral producTs (COCONUT) is an aggregated dataset comprising elucidated and predicted natural products (NPs) from open repositories. It offers a user-friendly web interface for browsing, searching, and efficiently downloading NPs. The latest database integrates more than 63 open NP resources, providing unrestricted access to data free of charge. Each entry in the database represents a "flat" NP structure, accompanied by information on its known stereochemical forms, relevant literature, producing organisms, natural geographical distribution, and precomputed molecular properties.

Summary of the COCONUT database's statistics:




Total Molecules
Total Collections
Unique Organisms
Citations Mapped




695,133
63
53,092


34,991





 

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




S.No
Database name
Entries integrated in COCONUT
Latest resource URL




1
AfroCancer
390
Fidele Ntie-Kang, Justina Ngozi Nwodo, Akachukwu Ibezim, Conrad Veranso Simoben, Berin Karaman, Valery Fuh Ngwa, Wolfgang Sippl, Michael Umale Adikwu, and Luc Meva’a Mbaze Journal of Chemical Information and Modeling 2014 54 (9), 2433-2450 https://doi.org/10.1021/ci5003697


2
AfroDB
953
Fidele 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. Efange https://doi.org/10.1371/journal.pone.0078085


3
AfroMalariaDB
265
Onguéné, 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


4
AnalytiCon Discovery NPs
5,147
Natural products are a sebset of AnalytiCon Discovery NPs https://ac-discovery.com/screening-libraries/


5
BIOFACQUIM
605
Pilón-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


6
BitterDB
685
Ayana 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


7
Carotenoids Database
1,195
Junko Yabuzaki, Carotenoids Database: structures, chemical fingerprints and distribution among organisms, Database, Volume 2017, 2017, bax004, https://doi.org/10.1093/database/bax004


8
ChEBI NPs
16,215
Janna 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


9
ChEMBL NPs
1,910
Anna 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


10
ChemSpider NPs
9,740
Harry E. Pence and Antony Williams Journal of Chemical Education 2010 87 (11), 1123-1124 https://doi.org/10.1021/ed100697w


11
CMAUP (cCollective molecular activities of useful plants)
47,593
Xian 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


12
ConMedNP
3,111
DOI https://doi.org/10.1039/C3RA43754J


13
ETM (Ethiopian Traditional Medicine) DB
1,798
Bultum, 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


14
Exposome-explorer
434
Vanessa 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


15
FoodDB
70,385
Natural products are a sebset of FoodDB https://foodb.ca/


16
GNPS (Global Natural Products Social Molecular Networking)
11,103
Wang, 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


17
HIM (Herbal Ingredients in-vivo Metabolism database)
1,259
Kang, 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


18
HIT (Herbal Ingredients Targets)
530
Hao 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


19
Indofine Chemical Company
46
Natural products are a sebset of Indofine Chemical Company https://indofinechemical.com/


20
InflamNat
664
Ruihan Zhang, Jing Lin, Yan Zou, Xing-Jie Zhang, and Wei-Lie Xiao Journal of Chemical Information and Modeling 2019 59 (1), 66-73 DOI: 10.1021/acs.jcim.8b00560 https://doi.org/10.1021/acs.jcim.8b00560


21
InPACdb
124
Vetrivel et al., Bioinformation 4(2): 71-74 (2009) https://www.bioinformation.net/004/001500042009.htm


22
InterBioScreen Ltd
68,372
Natural products are a sebset of InterBioScreen Ltd https://www.ibscreen.com/natural-compounds


23
KNApSaCK
48,241
Kensuke 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


24
Lichen Database
1,718
Olivier-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


25
Marine Natural Products
14,220
Gentile, 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


26
Mitishamba database
1,095
Derese, 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, Tanzania http://erepository.uonbi.ac.ke/handle/11295/92273


27
NANPDB (Natural Products from Northern African Sources)
7,482
Fidele 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 Günther Journal of Natural Products 2017 80 (7), 2067-2076 DOI: 10.1021/acs.jnatprod.7b00283 https://doi.org/10.1021/acs.jnatprod.7b00283


28
NCI DTP data
419
Natural products are a sebset of NCI DTP data https://wiki.nci.nih.gov/display/NCIDTPdata/Compound+Sets


29
NPACT
1,572
Manu 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


30
NPASS
96,173
Xian 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


31
NPAtlas
36,395
Jeffrey 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. Linington ACS Central Science 2019 5 (11), 1824-1833 DOI: 10.1021/acscentsci.9b00806 https://doi.org/10.1021/acscentsci.9b00806


32
NPCARE
1,446
Choi, 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


33
NPEdia
49,597
Takeshi 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


34
NuBBEDB
2,215
Pilon, 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


35
p-ANAPL
533
Fidele 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, 2014 https://doi.org/10.1371/journal.pone.0090655


36
Phenol-explorer
742
Joseph 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


37
PubChem NPs
3,533
Natural products are a sebset of PubChem NPs https://pubchem.ncbi.nlm.nih.gov/substance/251960601


38
ReSpect
4,854
Yuji 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.


39
SANCDB
995
Hatherley, 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


40
Seaweed Metabolite Database (SWMD)
1,075
Davis & Vasanthi, Bioinformation 5(8): 361-364 (2011) https://www.bioinformation.net/005/007900052011.htm


41
Specs Natural Products
744
Natural products are a sebset of Specs Natural Products https://www.specs.net/index.php


42
Spektraris NMR
248
Justin 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.


43
StreptomeDB
6,522
Aurélien 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


44
Super Natural II
325,149
Priyanka 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


45
TCMDB@Taiwan (Traditional Chinese Medicine database)
58,401
Calvin Yu-Chian Chen Published: January 6, 2011 https://doi.org/10.1371/journal.pone.0015939


46
TCMID (Traditional Chinese Medicine Integrated Database)
32,038
Xue 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.


47
TIPdb (database of Taiwan indigenous plants)
8,838
Chun-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


48
TPPT (Toxic Plants–PhytoToxins)
1,561
Barbara F. Günthardt, Juliane Hollender, Konrad Hungerbühler, Martin Scheringer, and Thomas D. Bucheli Journal of Agricultural and Food Chemistry 2018 66 (29), 7577-7588 DOI: 10.1021/acs.jafc.8b01639 https://pubs.acs.org/doi/10.1021/acs.jafc.8b01639


49
UEFS (Natural Products Databse of the UEFS)
503
Natural products are a sebset of UEFS (Natural Products Databse of the UEFS) https://zinc12.docking.org/catalogs/uefsnp


50
UNPD (Universal Natural Products Database)
213,210
Jiangyong Gu,Yuanshen Gui,Lirong Chen ,Gu Yuan,Hui-Zhe Lu,Xiaojie Xu Published: April 25, 2013 https://doi.org/10.1371/journal.pone.0062839


51
VietHerb
5,150
Thanh-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 Le Journal of Chemical Information and Modeling 2019 59 (1), 1-9 DOI: 10.1021/acs.jcim.8b00399 https://pubs.acs.org/doi/10.1021/acs.jcim.8b00399


52
ZINC NP
85,201
Teague Sterling and John J. Irwin Journal of Chemical Information and Modeling 2015 55 (11), 2324-2337 DOI: 10.1021/acs.jcim.5b00559 https://doi.org/10.1021/acs.jcim.5b00559


53
CyanoMetNP
2,113
Jones 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.


54
DrugBankNP
9,283
Wishart 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.


55
Australian natural products
21,591
Saubern, 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


56
EMNPD
6,145
Xu, 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


57
ANPDB
7,482
1) 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-Kang Molecular Informatics 2020 DOI: 10.1002/minf.202000163 https://doi.org/10.1002/minf.202000163 2) NANPDB: A Resource for Natural Products from Northern African Sources Fidele 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 Günther Journal of Natural Products 2017 DOI: 10.1021/acs.jnatprod.7b00283 https://pubs.acs.org/doi/10.1021/acs.jnatprod.7b00283


58
Phyto4Health
3,175
Nikita Ionov, Dmitry Druzhilovskiy, Dmitry Filimonov, and Vladimir Poroikov Journal of Chemical Information and Modeling 2023 63 (7), 1847-1851 DOI: 10.1021/acs.jcim.2c01567 https://pubs.acs.org/doi/10.1021/acs.jcim.2c01567


59
Piella DB
65
Natural products are a sebset of Piella DB https://micro.biol.ethz.ch/research/piel.html


60
Watermelon
1,526
Natural products are a sebset of Watermelon https://watermelon.naturalproducts.net/


61
Latin America dataset
12,959
Gómez-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.


62
CMNPD
31,561
Chuanyu 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


63
Supernatural3
1,203,509
Natural products are a sebset of Supernatural3 https://academic.oup.com/nar/article/51/D1/D654/6833249


 
Total Entries
2,551,803