Natural Product: NPC471404

Natural Product IDNPC471404
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YGKDPBLYDBVZMO-WQDCACQGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2431895
PubChem CID 72703240
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 YGKDPBLYDBVZMO-WQDCACQGSA-N
Standard InCHI InChI=1S/C45H34O16/c46-20-6-1-17(2-7-20)39-29(54)14-23-25(50)15-31-35(40(23)57-39)38-34-28(53)16-32-36(41(34)61-45(60-31,43(38)56)19-5-10-24(49)26(51)11-19)37-33-27(52)12-22(48)13-30(33)58-44(59-32,42(37)55)18-3-8-21(47)9-4-18/h1-13,15-16,29,37-39,42-43,46-56H,14H2/t29-,37+,38+,39+,42+,43+,44-,45+/m1/s1
SMILES C1C(C(OC2=C1C(=CC3=C2C4C(C(O3)(OC5=C4C(=CC6=C5C7C(C(O6)(OC8=CC(=CC(=C78)O)O)C9=CC=C(C=C9)O)O)O)C1=CC(=C(C=C1)O)O)O)O)C1=CC=C(C=C1)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
NPO32897 spenceria ramalana Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[24131240]
NPO32897 spenceria ramalana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT617 Organism Danio rerio Danio rerio Activity = 164.1 % PMID[15844965]
NPT617 Organism Danio rerio Danio rerio Activity = 157.7 % PMID[22372931]





 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 NPC471404 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
0.9265 High Similarity NPC134911
0.9143 High Similarity NPC478616
0.9143 High Similarity NPC478339
0.8714 High Similarity NPC46283
0.8714 High Similarity NPC469944
0.8676 High Similarity NPC155564
0.8571 High Similarity NPC272552
0.8571 High Similarity NPC226108
0.8571 High Similarity NPC322899
0.8082 Intermediate Similarity NPC44192
0.775 Intermediate Similarity NPC478337
0.775 Intermediate Similarity NPC478338
0.7692 Intermediate Similarity NPC147743
0.7692 Intermediate Similarity NPC4809
0.7692 Intermediate Similarity NPC73517
0.75 Intermediate Similarity NPC86630
0.7407 Intermediate Similarity NPC78074
0.7294 Intermediate Similarity NPC478617
0.7195 Intermediate Similarity NPC478340
0.7059 Intermediate Similarity NPC159526
0.6988 Remote Similarity NPC106601
0.6988 Remote Similarity NPC151474
0.6905 Remote Similarity NPC212614
0.6905 Remote Similarity NPC205613
0.6667 Remote Similarity NPC484331
0.6333 Remote Similarity NPC484330
0.6222 Remote Similarity NPC12326
0.5769 Remote Similarity NPC58190
0.5769 Remote Similarity NPC108811
0.5769 Remote Similarity NPC170103
0.5769 Remote Similarity NPC236202
0.5769 Remote Similarity NPC262911
0.5769 Remote Similarity NPC202742
0.5765 Remote Similarity NPC306267
0.5745 Remote Similarity NPC185231
0.5696 Remote Similarity NPC246202
0.5696 Remote Similarity NPC224161
0.5696 Remote Similarity NPC46335
0.5696 Remote Similarity NPC279406
0.5696 Remote Similarity NPC486519
0.5647 Remote Similarity NPC20050
0.5422 Remote Similarity NPC70409
0.5422 Remote Similarity NPC204770
0.5422 Remote Similarity NPC600551
0.5422 Remote Similarity NPC601980
0.5422 Remote Similarity NPC602065
0.5422 Remote Similarity NPC611024
0.5375 Remote Similarity NPC277331
0.5375 Remote Similarity NPC100482
0.5357 Remote Similarity NPC226809
0.5357 Remote Similarity NPC211561
0.5233 Remote Similarity NPC278548
0.5185 Remote Similarity NPC601999
0.5181 Remote Similarity NPC313116
0.5181 Remote Similarity NPC603340
0.5122 Remote Similarity NPC294558
0.5122 Remote Similarity NPC18185
0.5122 Remote Similarity NPC263940

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471404 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