Natural Product: NPC479061

Natural Product IDNPC479061
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UQUNGEHIRVREDL-QRHGVYBYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132584643
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 UQUNGEHIRVREDL-QRHGVYBYSA-N
Standard InCHI InChI=1S/C50H82O21/c1-9-12-18-21-30-22-19-16-14-13-15-17-20-23-32(52)66-41-34(54)31(24-51)65-50(70-42-35(55)33(53)27(6)61-48(42)64-30)44(41)71-49-43(68-46(60)26(5)11-3)38(58)40(29(8)63-49)69-47-37(57)36(56)39(28(7)62-47)67-45(59)25(4)10-2/h10-11,27-31,33-44,47-51,53-58H,9,12-24H2,1-8H3/b25-10+,26-11+/t27-,28-,29+,30+,31-,33-,34-,35+,36-,37-,38-,39+,40+,41+,42-,43-,44-,47+,48+,49+,50+/m1/s1
SMILES CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@@H]([C@@H](CO)O[C@H]([C@@H]2O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O[C@H]2[C@@H]([C@H]([C@H]([C@@H](C)O2)OC(=O)/C(=C/C)/C)O)O)O)OC(=O)/C(=C/C)/C)O[C@@H]2[C@H]([C@@H]([C@@H](C)O[C@H]2O1)O)O)O

  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
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota seeds n.a. n.a. PMID[22924480]
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota Seeds n.a. n.a. PMID[28006904]
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13214 Ipomoea alba Species Convolvulaceae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell line MCF7 Homo sapiens IC50 = 8000.0 nM PMID[28006904]
NPT83 Cell line MCF7 Homo sapiens IC50 = 16300.0 nM PMID[28006904]
NPT83 Cell line MCF7 Homo sapiens IC50 = 17000.0 nM PMID[28006904]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 11600.0 nM PMID[28006904]
NPT165 Cell line HeLa Homo sapiens IC50 = 9600.0 nM PMID[28006904]
NPT148 Cell line HCT-15 Homo sapiens IC50 = 9800.0 nM PMID[28006904]
NPT393 Cell line HCT-116 Homo sapiens IC50 = 15900.0 nM PMID[28006904]
NPT83 Cell line MCF7 Homo sapiens FC > 87.0 n.a. PMID[28006904]
NPT2 Others Unspecified n.a. FC > 1984.0 n.a. PMID[28006904]
NPT2 Others Unspecified n.a. FC > 2517.0 n.a. PMID[28006904]

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





 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 NPC479061 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
0.9865 High Similarity NPC479060
0.7326 Intermediate Similarity NPC238264
0.7326 Intermediate Similarity NPC477345
0.7059 Intermediate Similarity NPC109887
0.6882 Remote Similarity NPC475241
0.6774 Remote Similarity NPC477348
0.675 Remote Similarity NPC606819
0.6593 Remote Similarity NPC479057
0.6593 Remote Similarity NPC224953
0.6559 Remote Similarity NPC478728
0.6543 Remote Similarity NPC478729
0.6522 Remote Similarity NPC163409
0.6437 Remote Similarity NPC478734
0.6429 Remote Similarity NPC477330
0.6404 Remote Similarity NPC146992
0.6404 Remote Similarity NPC85759
0.6395 Remote Similarity NPC477349
0.6383 Remote Similarity NPC475164
0.6374 Remote Similarity NPC483170
0.6364 Remote Similarity NPC477344
0.6353 Remote Similarity NPC477329
0.6344 Remote Similarity NPC475525
0.6344 Remote Similarity NPC475540
0.6333 Remote Similarity NPC297768
0.6333 Remote Similarity NPC44682
0.6304 Remote Similarity NPC238056
0.6292 Remote Similarity NPC478733
0.6277 Remote Similarity NPC476066
0.6264 Remote Similarity NPC294748
0.6264 Remote Similarity NPC119583
0.6237 Remote Similarity NPC184915
0.6235 Remote Similarity NPC477328
0.6222 Remote Similarity NPC478722
0.618 Remote Similarity NPC479059
0.618 Remote Similarity NPC477326
0.6146 Remote Similarity NPC473605
0.6146 Remote Similarity NPC475375
0.6129 Remote Similarity NPC115013
0.6105 Remote Similarity NPC269318
0.6105 Remote Similarity NPC44782
0.6067 Remote Similarity NPC477331
0.6067 Remote Similarity NPC477332
0.6019 Remote Similarity NPC611287
0.6 Remote Similarity NPC472200
0.5962 Remote Similarity NPC600672
0.5962 Remote Similarity NPC610996
0.5957 Remote Similarity NPC477317
0.5957 Remote Similarity NPC477318
0.5895 Remote Similarity NPC183888
0.5895 Remote Similarity NPC126685
0.5889 Remote Similarity NPC89843
0.587 Remote Similarity NPC60849
0.5843 Remote Similarity NPC113745
0.5843 Remote Similarity NPC477320
0.5843 Remote Similarity NPC477323
0.5843 Remote Similarity NPC477325
0.5843 Remote Similarity NPC609436
0.5824 Remote Similarity NPC600446
0.5824 Remote Similarity NPC605013
0.5816 Remote Similarity NPC478727
0.5773 Remote Similarity NPC477347
0.5741 Remote Similarity NPC610997
0.5684 Remote Similarity NPC476087
0.5684 Remote Similarity NPC475667
0.5638 Remote Similarity NPC479058
0.5638 Remote Similarity NPC477319
0.5632 Remote Similarity NPC477350
0.5625 Remote Similarity NPC169345
0.5625 Remote Similarity NPC478732
0.5618 Remote Similarity NPC281563
0.5604 Remote Similarity NPC604005
0.5604 Remote Similarity NPC605014
0.5579 Remote Similarity NPC143421
0.5579 Remote Similarity NPC307400
0.5579 Remote Similarity NPC27289
0.5579 Remote Similarity NPC478730
0.5567 Remote Similarity NPC259294
0.5567 Remote Similarity NPC475270
0.5567 Remote Similarity NPC475327
0.5556 Remote Similarity NPC600721
0.5556 Remote Similarity NPC605872
0.5542 Remote Similarity NPC479056
0.5532 Remote Similarity NPC267592
0.5532 Remote Similarity NPC478725
0.5521 Remote Similarity NPC478726
0.5495 Remote Similarity NPC22742
0.5495 Remote Similarity NPC477346
0.5474 Remote Similarity NPC472205
0.5474 Remote Similarity NPC478723
0.5474 Remote Similarity NPC478724
0.5464 Remote Similarity NPC290012
0.5464 Remote Similarity NPC478731
0.5455 Remote Similarity NPC206823
0.5429 Remote Similarity NPC28069
0.5429 Remote Similarity NPC77651
0.5417 Remote Similarity NPC472204
0.5393 Remote Similarity NPC146380
0.5354 Remote Similarity NPC123204
0.5326 Remote Similarity NPC87153
0.5315 Remote Similarity NPC600940
0.5306 Remote Similarity NPC162925
0.5278 Remote Similarity NPC290276
0.5126 Remote Similarity NPC147032
0.5045 Remote Similarity NPC471025

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC479061 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