Natural Product: NPC473278

Natural Product IDNPC473278
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 [(2R,3R,4S,5R,6S)-3,5-Dihydroxy-6-[5-Hydroxy-2-(4-Hydroxyphenyl)-4-Oxochromen-7-Yl]Oxy-4-[(E)-3-(4-Hydroxyphenyl)Prop-2-Enoyl]Oxyoxan-2-Yl]Methyl (E)-3-Phenylprop-2-Enoate
IUPAC Name [(2R,3R,4S,5R,6S)-3,5-dihydroxy-6-[5-hydroxy-2-(4-hydroxyphenyl)-4-oxochromen-7-yl]oxy-4-[(E)-3-(4-hydroxyphenyl)prop-2-enoyl]oxyoxan-2-yl]methyl (E)-3-phenylprop-2-enoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL390638
PubChem CID 44429741
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 XLRROJNLELUHOS-FTJBIWNASA-N
Standard InCHI InChI=1S/C39H32O13/c40-25-12-6-23(7-13-25)9-17-34(45)52-38-36(46)32(21-48-33(44)16-8-22-4-2-1-3-5-22)51-39(37(38)47)49-27-18-28(42)35-29(43)20-30(50-31(35)19-27)24-10-14-26(41)15-11-24/h1-20,32,36-42,46-47H,21H2/b16-8+,17-9+/t32-,36-,37-,38+,39-/m1/s1
SMILES O=C(OC[C@H]1O[C@@H](Oc2cc(O)c3c(c2)oc(cc3=O)c2ccc(cc2)O)[C@@H]([C@H]([C@@H]1O)OC(=O)/C=C/c1ccc(cc1)O)O)/C=C/c1ccccc1

  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
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17287127]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6536 Marrubium velutinum Species Lamiaceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = 20.69 % PMID[17512741]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

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 NPC473278 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
0.8866 High Similarity NPC471030
0.7917 Intermediate Similarity NPC472994
0.7872 Intermediate Similarity NPC210961
0.7604 Intermediate Similarity NPC270675
0.7604 Intermediate Similarity NPC195685
0.6923 Remote Similarity NPC472993
0.6635 Remote Similarity NPC96605
0.6635 Remote Similarity NPC280642
0.6346 Remote Similarity NPC80068
0.6161 Remote Similarity NPC474093
0.6161 Remote Similarity NPC104910
0.6038 Remote Similarity NPC479765
0.6038 Remote Similarity NPC477629
0.5981 Remote Similarity NPC101636
0.5981 Remote Similarity NPC260504
0.5981 Remote Similarity NPC89809
0.5714 Remote Similarity NPC480796
0.5702 Remote Similarity NPC470716
0.566 Remote Similarity NPC64051
0.5636 Remote Similarity NPC484301
0.5596 Remote Similarity NPC188815
0.5556 Remote Similarity NPC139060
0.5537 Remote Similarity NPC199172
0.55 Remote Similarity NPC27942
0.549 Remote Similarity NPC220169
0.5405 Remote Similarity NPC298171
0.5377 Remote Similarity NPC44931
0.5364 Remote Similarity NPC205824
0.5357 Remote Similarity NPC179862
0.5308 Remote Similarity NPC475179
0.5289 Remote Similarity NPC241781
0.5253 Remote Similarity NPC331652
0.52 Remote Similarity NPC39360
0.52 Remote Similarity NPC29763
0.52 Remote Similarity NPC210003
0.5182 Remote Similarity NPC477628
0.5179 Remote Similarity NPC85751
0.5179 Remote Similarity NPC19240
0.5135 Remote Similarity NPC229409
0.5128 Remote Similarity NPC164704
0.5091 Remote Similarity NPC472992
0.5088 Remote Similarity NPC218161

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473278 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