Natural Product: NPC607913

Natural Product IDNPC607913
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KADCZAAXTVHSJI-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL349973
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 KADCZAAXTVHSJI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H16O8/c1-23-12-7-11(21)13-14(22)18(25-3)15(26-17(13)16(12)24-2)8-4-5-9(19)10(20)6-8/h4-7,19-21H,1-3H3
SMILES COc1cc(O)c2c(=O)c(OC)c(-c3ccc(O)c(O)c3)oc2c1OC

  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
NPO23963 Odixia angusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO57263 Ozothamnus lycopodioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO56658 Calceolaria tenella Species Calceolariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63128 Calycadenia ciliosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53149 Calycadenia multiglandulosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8790 Cyanostegia angustifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44707 Hemizonia spp. Genus Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52441 Madia anomala Genus Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13631 Microglossa pyrifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO56203 Ricinocarpos muricatus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8790 Cyanostegia angustifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8790 Cyanostegia angustifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13631 Microglossa pyrifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23963 Odixia angusta Species Asteraceae 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
NPT29317 Organism Enterovirus C Enterovirus C Minimal dose = 0.5 ug ml-1 PMID[1847431]
NPT29317 Organism Enterovirus C Enterovirus C ED99 = 0.2 ug ml-1 PMID[1847431]
NPT29317 Organism Enterovirus C Enterovirus C Reduction factor = 100000.0 n.a. PMID[1847431]
NPT30043 Cell line Vero Chlorocebus sabaeus CyD50 > 5.0 ug ml-1 PMID[1847431]
NPT1538 Organism Human rhinovirus sp. Human rhinovirus sp. CyD50 = 20.0 ug ml-1 PMID[1847431]
NPT1538 Organism Human rhinovirus sp. Human rhinovirus sp. ED99 = 2.0 ug ml-1 PMID[1847431]

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
Enterovirus C Enterovirus C Max non-toxic dose = 10.0 ug ml-1 PMID[1847431]

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 NPC607913 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
0.8235 Intermediate Similarity NPC605144
0.7778 Intermediate Similarity NPC603112
0.7692 Intermediate Similarity NPC189960
0.7636 Intermediate Similarity NPC152166
0.7547 Intermediate Similarity NPC32557
0.7273 Intermediate Similarity NPC178854
0.7222 Intermediate Similarity NPC176665
0.7091 Intermediate Similarity NPC22472
0.6909 Remote Similarity NPC188871
0.6667 Remote Similarity NPC603082
0.6607 Remote Similarity NPC130894
0.6429 Remote Similarity NPC287979
0.6316 Remote Similarity NPC286342
0.6207 Remote Similarity NPC18772
0.6129 Remote Similarity NPC259411
0.6081 Remote Similarity NPC265115
0.6034 Remote Similarity NPC214138
0.6034 Remote Similarity NPC163524
0.5932 Remote Similarity NPC305663
0.5921 Remote Similarity NPC480466
0.5763 Remote Similarity NPC149127
0.5763 Remote Similarity NPC105242
0.5763 Remote Similarity NPC146679
0.5763 Remote Similarity NPC606763
0.569 Remote Similarity NPC606920
0.5593 Remote Similarity NPC306821
0.5574 Remote Similarity NPC253634
0.55 Remote Similarity NPC301123
0.55 Remote Similarity NPC260895
0.55 Remote Similarity NPC610660
0.5484 Remote Similarity NPC4481
0.5424 Remote Similarity NPC245546
0.541 Remote Similarity NPC86485
0.5397 Remote Similarity NPC19687
0.5397 Remote Similarity NPC78326
0.5333 Remote Similarity NPC191459
0.5333 Remote Similarity NPC103904
0.5333 Remote Similarity NPC262094
0.5333 Remote Similarity NPC103342
0.5333 Remote Similarity NPC292107
0.5323 Remote Similarity NPC270620
0.5323 Remote Similarity NPC265511
0.5246 Remote Similarity NPC87125
0.5246 Remote Similarity NPC76376
0.5246 Remote Similarity NPC143828
0.5238 Remote Similarity NPC58382
0.5238 Remote Similarity NPC235215
0.5238 Remote Similarity NPC236769
0.5238 Remote Similarity NPC7846
0.5161 Remote Similarity NPC108406
0.5161 Remote Similarity NPC201136
0.5161 Remote Similarity NPC32420
0.5152 Remote Similarity NPC480464
0.5128 Remote Similarity NPC355481
0.5079 Remote Similarity NPC204854
0.5072 Remote Similarity NPC76833
0.5067 Remote Similarity NPC84362

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607913 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