Natural Product: NPC611191| Natural Product ID | NPC611191 |
|
Common Name
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
| VEFSVJGWJQPWFS-ZXKKMYOJSA-N |
| IUPAC Name | n.a. |
| Synonyms | |
| Synthetic Gene Cluster | n.a. |
| ChEMBL Identifier | CHEMBL4294164 |
| PubChem CID | n.a. |
| Chemical Classification |
|
The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.
Chemical Representations
| Standard InCHIKey | VEFSVJGWJQPWFS-ZXKKMYOJSA-N |
| Standard InCHI | InChI=1S/C43H66O14/c1-10-21(2)36(53)57-34-33(50)43(20-54-22(3)45)24(17-38(34,4)5)23-11-12-26-39(6)15-14-28(55-37-31(49)29(47)30(48)32(56-37)35(51)52)40(7,19-44)25(39)13-16-41(26,8)42(23,9)18-27(43)46/h10-11,24-34,37,44,46-50H,12-20H2,1-9H3,(H,51,52)/b21-10+/t24-,25+,26+,27-,28-,29-,30-,31+,32-,33-,34-,37+,39-,40-,41+,42+,43-/m0/s1 |
| SMILES | C/C=C(C)C(=O)O[C@H]1[C@H](O)[C@]2(COC(C)=O)[C@@H](O)C[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@H](O[C@@H]6O[C@H](C(=O)O)[C@@H](O)[C@H](O)[C@H]6O)[C@@](C)(CO)[C@@H]5CC[C@]43C)[C@@H]2CC1(C)C |
  Calculated Properties
  Species Source| Organism ID | Organism Name | Taxonomy Level | Family | SuperKingdom | Isolation Part | Collection Location | Collection Time | Reference |
|---|---|---|---|---|---|---|---|---|
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1007/s11274-011-0870-8] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1007/s11627-014-9655-8] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[COCONUT] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
| NPO29166 | Gymnema sylvestre | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].
  NP Quantity Composition/Concentration| Organism ID | Organism Name | Organism Material Preparation | Organism Part | NP Quantity (Standard) | NP Quantity (Minimum) | NP Quantity (Maximum) | Quantity Unit | Reference |
|---|
Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].
Biological Activity
| Target ID | Target Type | Target Name | Target Organism | Activity Type | Activity Relation | Value | Unit | Reference |
|---|---|---|---|---|---|---|---|---|
| NPT1429 | Individual protein | Heat shock protein HSP 90-beta | Homo sapiens | Ratio | = | 0.737 | n.a. | PMID[28256837] |
| NPT1224 | Individual protein | Glyceraldehyde-3-phosphate dehydrogenase liver | Homo sapiens | Ratio | = | 0.524 | n.a. | PMID[28256837] |
| NPT2604 | Individual protein | Heat shock cognate 71 kDa protein | Homo sapiens | Ratio | = | 0.615 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.448 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.527 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.238 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.33 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.313 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.818 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.39 | n.a. | PMID[28256837] |
| NPT28441 | Single protein | Elongation factor 1-beta | Homo sapiens | Ratio | = | 0.525 | n.a. | PMID[28256837] |
| NPT4718 | Individual protein | Transketolase | Homo sapiens | Ratio | = | 0.623 | n.a. | PMID[28256837] |
| NPT27115 | Single protein | Heat shock protein HSP 60 | Homo sapiens | Ratio | = | 0.57 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.075 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.105 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.245 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.062 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.173 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.255 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.114 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.069 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.453 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.332 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.27 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.16 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.269 | n.a. | PMID[28256837] |
| NPT26015 | Single protein | 14-3-3 protein zeta/delta | Homo sapiens | Ratio | = | 0.62 | n.a. | PMID[28256837] |
| NPT28128 | Single protein | Peroxiredoxin-1 | Homo sapiens | Ratio | = | 1.059 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.396 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.439 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.119 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Activity | n.a. | n.a. | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.405 | n.a. | PMID[28256837] |
| NPT28154 | Protein nucleic-acid complex | 80S Ribosome | Homo sapiens | Ratio | = | 0.158 | n.a. | PMID[28256837] |
| NPT29751 | Single protein | Poly(rC)-binding protein 2 | Homo sapiens | Ratio | = | 0.633 | n.a. | PMID[28256837] |
| NPT29765 | Single protein | Rho-related GTP-binding protein RhoQ | Homo sapiens | Ratio | = | 0.706 | n.a. | PMID[28256837] |
| NPT29004 | Single protein | Elongation factor 1-alpha 1 | Homo sapiens | Ratio | = | 0.629 | n.a. | PMID[28256837] |
| NPT888 | Individual protein | 78 kDa glucose-regulated protein | Homo sapiens | Ratio | = | 0.527 | n.a. | PMID[28256837] |
| NPT29227 | Single protein | 40S ribosomal protein S6 | Homo sapiens | Ratio | = | 0.317 | n.a. | PMID[28256837] |
| NPT29847 | Single protein | Programmed cell death protein 6 | Homo sapiens | Ratio | = | 0.68 | n.a. | PMID[28256837] |
| NPT29347 | Single protein | Elongation factor 1-delta | Homo sapiens | Ratio | = | 0.622 | n.a. | PMID[28256837] |
| NPT29460 | Single protein | Phosphate carrier protein, mitochondrial | Homo sapiens | Ratio | = | 0.57 | n.a. | PMID[28256837] |
| NPT25569 | Single protein | D-3-phosphoglycerate dehydrogenase | Homo sapiens | Ratio | = | 0.509 | n.a. | PMID[28256837] |
| NPT28631 | Single protein | Alpha enolase | Homo sapiens | Ratio | = | 0.811 | n.a. | PMID[28256837] |
| NPT30107 | Single protein | Amyloid-beta A4 protein | Homo sapiens | Ratio | = | 0.744 | n.a. | PMID[28256837] |
| NPT29366 | Single protein | Elongation factor 2 | Homo sapiens | Ratio | = | 0.688 | n.a. | PMID[28256837] |
| NPT29877 | Single protein | Stress-70 protein, mitochondrial | Homo sapiens | Ratio | = | 0.751 | n.a. | PMID[28256837] |
| NPT30141 | Single protein | Vimentin | Homo sapiens | Ratio | = | 0.817 | n.a. | PMID[28256837] |
| NPT29366 | Single protein | Elongation factor 2 | Homo sapiens | Ratio | = | 0.795 | n.a. | PMID[28256837] |
| NPT28822 | Single protein | Tubulin alpha-1B chain | Homo sapiens | Ratio | = | 0.523 | n.a. | PMID[28256837] |
| NPT29644 | Single protein | Putative annexin A2-like protein | Homo sapiens | Ratio | = | 0.988 | n.a. | PMID[28256837] |
| NPT26205 | Single protein | Eukaryotic initiation factor 4A-II | Homo sapiens | Ratio | = | 0.404 | n.a. | PMID[28256837] |
| NPT6402 | Individual protein | Tubulin beta-5 chain | Homo sapiens | Ratio | = | 0.52 | n.a. | PMID[28256837] |
| NPT28898 | Single protein | Alkyldihydroxyacetonephosphate synthase, peroxisomal | Homo sapiens | Ratio | = | 0.955 | n.a. | PMID[28256837] |
| NPT29764 | Single protein | 60S acidic ribosomal protein P2 | Homo sapiens | Ratio | = | 0.329 | n.a. | PMID[28256837] |
| NPT28972 | Single protein | 40S ribosomal protein S27 | Homo sapiens | Ratio | = | 0.418 | n.a. | PMID[28256837] |
| NPT30015 | Single protein | Phosphoglycerate kinase 1 | Homo sapiens | Ratio | = | 0.665 | n.a. | PMID[28256837] |
| NPT29391 | Single protein | Elongation factor 1-gamma | Homo sapiens | Ratio | = | 0.536 | n.a. | PMID[28256837] |
| NPT644 | Individual protein | L-lactate dehydrogenase A chain | Homo sapiens | Ratio | = | 0.48 | n.a. | PMID[28256837] |
| NPT26522 | Single protein | Ras-related protein Rab-7a | Homo sapiens | Ratio | = | 0.568 | n.a. | PMID[28256837] |
| NPT28724 | Single protein | Putative tubulin-like protein alpha-4B | Homo sapiens | Ratio | = | 0.423 | n.a. | PMID[28256837] |
| NPT5887 | Individual protein | Cyclophilin A | Homo sapiens | Ratio | = | 1.205 | n.a. | PMID[28256837] |
| NPT30051 | Single protein | Actin, cytoplasmic 1 | Homo sapiens | Ratio | = | 0.436 | n.a. | PMID[28256837] |
| NPT24326 | Single protein | GTP-binding nuclear protein Ran | Homo sapiens | Ratio | = | 1.535 | n.a. | PMID[28256837] |
| NPT52 | Individual protein | Pyruvate kinase isozymes M1/M2 | Homo sapiens | Ratio | = | 0.899 | n.a. | PMID[28256837] |
| Target ID | Target Type | Target Name | Target Organism | Activity Type | Activity Relation | Value | Unit | Reference |
|---|---|---|---|---|---|---|---|---|
| NPT165 | Cell line | HeLa | Homo sapiens | Inhibition | n.a. | n.a. | % | PMID[28256837] |
| NPT28438 | Unchecked | Unchecked | n.a. | Ratio | = | 0.509 | n.a. | PMID[28256837] |
| NPT28438 | Unchecked | Unchecked | n.a. | Inhibition | n.a. | n.a. | % | PMID[28256837] |
| NPT28729 | Protein family | Trypsin | Homo sapiens | Ratio | = | 1.0 | n.a. | PMID[28256837] |
| Target ID | Target Type | Target Name | Target Organism | Activity Type | Activity Relation | Value | Unit | Reference |
|---|
Experimental ADME
| Experiment Model | Experiment Tissue | ADME Type | ADME Relation | ADME Value | ADME Unit | Reference |
|---|---|---|---|---|---|---|
| Homo sapiens | n.a. | Drug uptake | = | 4.0 | % | PMID[28256837] |
Experimental Toxicity
| Experiment Model | Experiment Organism | Toxicity Type | Toxicity Relation | Toxicity Value | Toxicity Unit | Reference |
|---|
Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria
| Hepatotoxicity | Carcinogenicity | Mutagenicity | Cardiotoxicity | Respiratory Toxicity | Eye Irritation | Endocrine Disruption |
|---|---|---|---|---|---|---|
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Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]
  Chemically structural similarityTop-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)
Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.
●  The left chart: Distribution of similarity level between NPC611191 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).
| Similarity Score | Similarity Level | Natural Product ID |
|---|---|---|
| 0.7387 | Intermediate Similarity | NPC252289 |
| 0.7387 | Intermediate Similarity | NPC305793 |
| 0.7094 | Intermediate Similarity | NPC11577 |
| 0.7094 | Intermediate Similarity | NPC141600 |
| 0.7034 | Intermediate Similarity | NPC476775 |
| 0.6759 | Remote Similarity | NPC603832 |
| 0.6579 | Remote Similarity | NPC1314 |
| 0.6579 | Remote Similarity | NPC273878 |
| 0.6371 | Remote Similarity | NPC476778 |
| 0.6339 | Remote Similarity | NPC477191 |
| 0.632 | Remote Similarity | NPC476776 |
| 0.63 | Remote Similarity | NPC224121 |
| 0.6261 | Remote Similarity | NPC472267 |
| 0.6261 | Remote Similarity | NPC115656 |
| 0.6134 | Remote Similarity | NPC269484 |
| 0.6134 | Remote Similarity | NPC97918 |
| 0.6066 | Remote Similarity | NPC476774 |
| 0.6 | Remote Similarity | NPC477192 |
| 0.5932 | Remote Similarity | NPC609119 |
| 0.5862 | Remote Similarity | NPC477193 |
| 0.5798 | Remote Similarity | NPC252657 |
| 0.5798 | Remote Similarity | NPC88311 |
| 0.5772 | Remote Similarity | NPC82380 |
| 0.5772 | Remote Similarity | NPC478597 |
| 0.5772 | Remote Similarity | NPC244296 |
| 0.5763 | Remote Similarity | NPC477195 |
| 0.5714 | Remote Similarity | NPC107536 |
| 0.5714 | Remote Similarity | NPC280029 |
| 0.5714 | Remote Similarity | NPC9470 |
| 0.5714 | Remote Similarity | NPC477196 |
| 0.568 | Remote Similarity | NPC478596 |
| 0.5676 | Remote Similarity | NPC473884 |
| 0.5615 | Remote Similarity | NPC279915 |
| 0.5556 | Remote Similarity | NPC476780 |
| 0.5546 | Remote Similarity | NPC477194 |
| 0.5514 | Remote Similarity | NPC480937 |
| 0.5487 | Remote Similarity | NPC475171 |
| 0.5478 | Remote Similarity | NPC11551 |
| 0.5455 | Remote Similarity | NPC283343 |
| 0.54 | Remote Similarity | NPC258547 |
| 0.536 | Remote Similarity | NPC602995 |
| 0.5354 | Remote Similarity | NPC470518 |
| 0.5328 | Remote Similarity | NPC25998 |
| 0.531 | Remote Similarity | NPC482748 |
| 0.5268 | Remote Similarity | NPC603870 |
| 0.5159 | Remote Similarity | NPC603137 |
| 0.5154 | Remote Similarity | NPC271610 |
| 0.513 | Remote Similarity | NPC157868 |
| 0.5124 | Remote Similarity | NPC477079 |
| 0.5122 | Remote Similarity | NPC605294 |
| 0.512 | Remote Similarity | NPC478600 |
| 0.512 | Remote Similarity | NPC478599 |
| 0.5115 | Remote Similarity | NPC478153 |
| 0.5093 | Remote Similarity | NPC286347 |
| 0.5091 | Remote Similarity | NPC294112 |
| 0.5076 | Remote Similarity | NPC476777 |
| 0.5043 | Remote Similarity | NPC242840 |
| 0.5039 | Remote Similarity | NPC329828 |
Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.
●  The left chart: Distribution of similarity level between NPC611191 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).
| Similarity Score | Similarity Level | Drug ID | Developmental Stage |
|---|---|---|---|
| NPD |
  Bioactivity similaritySimilarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.
