Natural Product: NPC610359

Natural Product IDNPC610359
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YSXLGTWJLNLXKQ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL189626
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 YSXLGTWJLNLXKQ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H18O8/c1-23-13-5-9(6-14(24-2)18(13)25-3)17-19(26-4)16(22)15-11(21)7-10(20)8-12(15)27-17/h5-8,20-21H,1-4H3
SMILES COc1cc(-c2oc3cc(O)cc(O)c3c(=O)c2OC)cc(OC)c1OC

  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
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota roots Gabon 1987 PMID[18327911]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[18327911]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[26938998]
NPO57221 Adina cordifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44869 Cistus albanicus Species Cistaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51609 Cistus symphytifolius Species Cistaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63478 Betula nigra Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28528 Bridelia ferruginea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55655 Gutierrezia alamanii Genus Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28528 Bridelia ferruginea Species Phyllanthaceae 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
NPT139 Cell line HT-29 Homo sapiens Activity = 101.8 n.a. PMID[15828817]
NPT139 Cell line HT-29 Homo sapiens Activity = 101.9 n.a. PMID[15828817]

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 NPC610359 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
0.7925 Intermediate Similarity NPC162351
0.7925 Intermediate Similarity NPC603596
0.75 Intermediate Similarity NPC123886
0.75 Intermediate Similarity NPC184536
0.75 Intermediate Similarity NPC103342
0.7358 Intermediate Similarity NPC286342
0.7358 Intermediate Similarity NPC59951
0.7308 Intermediate Similarity NPC472438
0.717 Intermediate Similarity NPC219330
0.7143 Intermediate Similarity NPC279989
0.7091 Intermediate Similarity NPC82325
0.7037 Intermediate Similarity NPC62536
0.7037 Intermediate Similarity NPC76376
0.6667 Remote Similarity NPC607530
0.65 Remote Similarity NPC158874
0.6207 Remote Similarity NPC29841
0.6102 Remote Similarity NPC606638
0.6102 Remote Similarity NPC609179
0.6094 Remote Similarity NPC97255
0.6071 Remote Similarity NPC7973
0.6034 Remote Similarity NPC600900
0.5932 Remote Similarity NPC115798
0.5932 Remote Similarity NPC159103
0.5926 Remote Similarity NPC181250
0.5909 Remote Similarity NPC470458
0.5909 Remote Similarity NPC269285
0.5862 Remote Similarity NPC50403
0.5862 Remote Similarity NPC28274
0.5846 Remote Similarity NPC259632
0.5833 Remote Similarity NPC12200
0.5738 Remote Similarity NPC133953
0.569 Remote Similarity NPC266960
0.5667 Remote Similarity NPC54394
0.5593 Remote Similarity NPC241838
0.5593 Remote Similarity NPC78341
0.5593 Remote Similarity NPC120464
0.5593 Remote Similarity NPC163524
0.5593 Remote Similarity NPC483773
0.5593 Remote Similarity NPC601901
0.5574 Remote Similarity NPC235215
0.5574 Remote Similarity NPC236769
0.5574 Remote Similarity NPC206604
0.5522 Remote Similarity NPC56786
0.55 Remote Similarity NPC9609
0.5493 Remote Similarity NPC470461
0.5484 Remote Similarity NPC125062
0.5479 Remote Similarity NPC325555
0.5479 Remote Similarity NPC226304
0.5439 Remote Similarity NPC602291
0.5424 Remote Similarity NPC203891
0.5417 Remote Similarity NPC470460
0.541 Remote Similarity NPC176300
0.5333 Remote Similarity NPC214138
0.5333 Remote Similarity NPC231772
0.5333 Remote Similarity NPC146679
0.5333 Remote Similarity NPC101830
0.5323 Remote Similarity NPC7846
0.5323 Remote Similarity NPC52005
0.5246 Remote Similarity NPC18772
0.5238 Remote Similarity NPC183950
0.5205 Remote Similarity NPC265530
0.5172 Remote Similarity NPC179271
0.5167 Remote Similarity NPC287979
0.5167 Remote Similarity NPC103904
0.5167 Remote Similarity NPC262094
0.5156 Remote Similarity NPC483775
0.5152 Remote Similarity NPC153512
0.5152 Remote Similarity NPC99671
0.5147 Remote Similarity NPC183
0.5143 Remote Similarity NPC54802
0.5143 Remote Similarity NPC197304
0.5139 Remote Similarity NPC63454
0.5139 Remote Similarity NPC183851
0.5132 Remote Similarity NPC609478
0.5082 Remote Similarity NPC110070
0.5082 Remote Similarity NPC149127
0.5082 Remote Similarity NPC260895
0.5082 Remote Similarity NPC105242
0.5082 Remote Similarity NPC176665
0.5082 Remote Similarity NPC188871
0.5079 Remote Similarity NPC25495
0.5079 Remote Similarity NPC78302
0.5079 Remote Similarity NPC58382
0.5077 Remote Similarity NPC605634
0.507 Remote Similarity NPC288084
0.507 Remote Similarity NPC276222
0.507 Remote Similarity NPC274618
0.507 Remote Similarity NPC34531
0.507 Remote Similarity NPC118284
0.507 Remote Similarity NPC608147
0.5067 Remote Similarity NPC472459
0.5065 Remote Similarity NPC223747

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC610359 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