Natural Product: NPC261333

Natural Product IDNPC261333
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Rabdoserrin B
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL470763
PubChem CID 14466844
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane diterpenoids

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 NKQVWQVQOKOKNW-WEMBNSTNSA-N
Standard InCHI InChI=1S/C20H30O6/c1-9-15-10(22)6-12-19(8-21)11(18(2,3)5-4-13(19)23)7-14(24)20(12,16(9)25)17(15)26/h10-15,17,21-24,26H,1,4-8H2,2-3H3/t10-,11+,12-,13-,14+,15+,17+,19+,20-/m0/s1
SMILES OC[C@]12[C@@H](O)CCC([C@H]2C[C@H]([C@]23[C@H]1C[C@H](O)[C@H]([C@H]2O)C(=C)C3=O)O)(C)C

  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
NPO17628 Rabdosia excisa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[15043413]
NPO8282 Physalis viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15730264]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17580910]
NPO6895 Elateriospermum tapos Species Euphorbiaceae Eukaryota leaves and stem Nakorn Si Thammarat Province, Thailand 2004-MAR PMID[18179177]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[21954931]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23270478]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[25396337]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[27295506]
NPO26123 Isodon serra Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32993289]
NPO458 Ophiarachna incrassata Species Ophiodermatidae Eukaryota n.a. n.a. n.a. PMID[7853009]
NPO74 Artemisia indica Species Asteraceae Eukaryota n.a. stem n.a. PMID[9748386]
NPO17628 Rabdosia excisa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10263 Alternaria tagetica Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2313 Jungia spectabilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26123 Isodon serra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20759 Isodon inflexa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6318 Caulerpa flexilis Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO458 Ophiarachna incrassata Species Ophiodermatidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4989 Tricholoma orirubens Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20759 Isodon inflexa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17628 Rabdosia excisa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17628 Rabdosia excisa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26123 Isodon serra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20759 Isodon inflexa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2248 Aiphanes horrida Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27832 Pyrobaculum neutrophilum Species Thermoproteaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO74 Artemisia indica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26123 Isodon serra Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4989 Tricholoma orirubens Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6318 Caulerpa flexilis Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1361 Chenopodium vulvaria Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17628 Rabdosia excisa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6895 Elateriospermum tapos Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8282 Physalis viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4530 Erysimum marschallianum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2248 Aiphanes horrida Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1680 Physalis angulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2313 Jungia spectabilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14622 Micromonospora lacustris Species Micromonosporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19924 Trachycladiella aurea Species Meteoriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10263 Alternaria tagetica Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO458 Ophiarachna incrassata Species Ophiodermatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3591 Halleria lucida Species Stilbaceae 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
NPT168 Cell line P388 Mus musculus IC50 = 1.01 ug.mL-1 PMID[15043413]

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 NPC261333 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
0.7447 Intermediate Similarity NPC101233
0.7 Intermediate Similarity NPC144739
0.68 Remote Similarity NPC104371
0.68 Remote Similarity NPC215271
0.64 Remote Similarity NPC153775
0.64 Remote Similarity NPC129004
0.64 Remote Similarity NPC29247
0.64 Remote Similarity NPC289539
0.6275 Remote Similarity NPC91772
0.5556 Remote Similarity NPC135548
0.537 Remote Similarity NPC181594
0.5273 Remote Similarity NPC291785
0.5185 Remote Similarity NPC138245
0.5091 Remote Similarity NPC127408

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC261333 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