Natural Product: NPC611191

Natural Product IDNPC611191
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
  • CHEMONTID:0000000 [Organic compounds]

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

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  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

Molecular-level 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]

In vitro activity

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]

In vivo activity

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

Quantitative 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

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 similarity

Similar Active Natural Products in NPASS

Top-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

Similar Clinical/Approved Drugs

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 similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity 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.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data