The Therapeutic Drug Target Database Human SwissProt

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This dataset is a selection of The Therapeutic Target Database (release 4.3.02, 18th Oct 2013) protein IDs for successful targets. The web page states 388 but these reduced to 345 human Swiss-Prot accessions.

Complexity

Therapeutic Target Database (TTD) is a database where this dataset on The Therapeutic Drug Target Database Human SwissProt was extracted. The links provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. The links also include relevant databases from HGNC and CHeMDL containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.

The dataset includes utilities that can be explored; there are two that might be considered: a) following the database links and b) comparing them for intersects (protein IDs in common) and differentials (protein IDs unique to particular lists or subsets). The information extends to comparisons with lists that can be generated in the course of other studies or other published work (e.g. expression data or disease association gene candidates). Other areas that can be explored are: a) what other utilities that are found valuable and b) other recently published target lists recommended for inclusion.

The metadata descriptions from this source are minimal since context is provided either in the references and/or the download descriptions for the appropriate databases or sources. The lists are Excel sheets of UniProtKB, HGNC and ChEMBL live links.

Lists that are not UniProtKB Accessions in the first place are normalized to these (e.g. mappings of Human Gene Nomenclature Committee (HGNC) Symbols or Entrez Gene IDs (EGID) to UniProtKB). They are then filtered to human and Swiss-Prot (i.e. any TrEMBL entries are removed) and to approved drug targets if this is an option in the original list. In such cases lists that are hosted thus become transformations, rather than direct facsimiles, of the primary sources.

Given such ID cross-mappings are not perfect; absolute correctness is not guaranteed. However, International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS) Guide to PHARMACOLOGY versions are supplied in good faith and the originals are available in every case.

If readers are unfamiliar with protein list “slicing and dicing” the source recommends the following:

1. The UniProtKB interface
2. Venny (for comparing up to four lists)
3. Panther (for displaying detailed protein classifications and attributes from lists)

“Knowledge and investigation of therapeutic targets (responsible for drug efficacy) and the targeted drugs facilitate target and drug discovery and validation. Therapeutic Target Database (TTD) has been developed to provide comprehensive information about efficacy targets and the corresponding approved, clinical trial and investigative drugs. Since its last update, major improvements and updates have been made to TTD. In addition to the significant increase of data content (from 1894 targets and 5028 drugs to 2025 targets and 17,816 drugs), we added target validation information (drug potency against target, effect against disease models and effect of target knockout, knockdown or genetic variations) for 932 targets, and 841 quantitative structure activity relationship models for active compounds of 228 chemical types against 121 targets. Moreover, we added the data from our previous drug studies including 3681 multi-target agents against 108 target pairs, 116 drug combinations with their synergistic, additive, antagonistic, potentiative or reductive mechanisms, 1427 natural product-derived approved, clinical trial and pre-clinical drugs and cross-links to the clinical trial information page in the ClinicalTrials.gov database for 770 clinical trial drugs. These updates are useful for facilitating target discovery and validation, drug lead discovery and optimization, and the development of multi-target drugs and drug combinations.” PubMed Abstract on Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery, Epub 2011 Sep 24.

Date Created

2011-08-25

Last Modified

27/01/2017

Version

27/01/2017

Update Frequency

Irregular

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs => International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS) Guide to PHARMACOLOGY

Source License URL

John Snow Labs Standard License

Source License Requirements

The Guide to PHARMACOLOGY database is licensed under the Open Data Commons Open Database License (ODbL). Its contents are licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported license.

Source Citation

Zhu F, Shi Z, Qin C, Tao L, Liu X, Xu F, Zhang L, Song Y, Liu XH, Zhang JX, Han BC, Zhang P, Chen YZ. Therapeutic target database update 2012 a resource for facilitating target-oriented drug discovery. Nucleic Acids Res. 40(D1) D1128-1136, 2012. PubMed.

Keywords

Drug Target Database, Drug Targets, Protein Database, TTD, Drug Bank, DrugDev, Druggable Targets Database, Drug Interaction Database, Drug Database

Other Titles

The Therapeutic Drug Target Database, The Drug Targets Database Human SwissProt, TTD Target Database Human SwissProt, The Therapeutic Drug Bank Target Database Human SwissProt, The Therapeutic Drug Database Human SwissProt

Name Description Type Constraints
UniProtKB_EntryThis subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.stringrequired : 1
Protein_NamesThis subsection of the Protein Names on ‘Names and Taxonomy’ section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein. This subsection may also include information on the activity of the protein, such as a precise description of the catalytic mechanism of enzymes, or information about individual protein chains or functional domains contained within it, if pertinent.stringrequired : 1
Cross_Reference_HGNC_IDHGNC ID for each protein name.stringrequired : 1
HGNC_LinkLinks to the HGNC databases cross-referenced in UniProtKB Swiss-Prot > HGNCstringrequired : 1
Cross_Reference_ChEMBL_IDChEMBL ID for each protein name.string-
ChEMBL_LinkLinks to the ChEMBL databases cross-referenced in UniProtKB Swiss-Prot > CHeMBLstring-
UniProtKB_EntryProtein_NamesCross_Reference_HGNC_IDHGNC_LinkCross_Reference_ChEMBL_IDChEMBL_Link
P05546Heparin cofactor 2HGNC:4838, SERPIND1http://www.genenames.org/data/hgnc_data.php?hgnc_id=4838
Q92736Ryanodine receptor 2HGNC:10484, RYR2http://www.genenames.org/data/hgnc_data.php?hgnc_id=10484
P41439Folate receptor gammaHGNC:3795, FOLR3http://www.genenames.org/data/hgnc_data.php?hgnc_id=3795
P01009Alpha-1-antitrypsinHGNC:8941, SERPINA1http://www.genenames.org/data/hgnc_data.php?hgnc_id=8941
P53004Biliverdin reductase AHGNC:1062, BLVRAhttp://www.genenames.org/data/hgnc_data.php?hgnc_id=1062
P12235ADP/ATP translocase 1HGNC:10990, SLC25A4http://www.genenames.org/data/hgnc_data.php?hgnc_id=10990
P22830Ferrochelatase, mitochondrialHGNC:3647, FECHhttp://www.genenames.org/data/hgnc_data.php?hgnc_id=3647
P54802Alpha-N-acetylglucosaminidaseHGNC:7632, NAGLUhttp://www.genenames.org/data/hgnc_data.php?hgnc_id=7632
P06126T-cell surface glycoprotein CD1aHGNC:1634, CD1Ahttp://www.genenames.org/data/hgnc_data.php?hgnc_id=1634
P49913Cathelicidin antimicrobial peptideHGNC:1472, CAMPhttp://www.genenames.org/data/hgnc_data.php?hgnc_id=1472