Natural Product: NPC108954

Natural Product IDNPC108954
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IMSLBKHRWPJCJZ-JILLZZLSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101282628
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 IMSLBKHRWPJCJZ-JILLZZLSSA-N
Standard InCHI InChI=1S/C25H42O2/c1-16(15-26)17-9-13-25(6)19-7-8-20-22(2,3)21(27)11-12-23(20,4)18(19)10-14-24(17,25)5/h16-17,20-21,26-27H,7-15H2,1-6H3/t16-,17-,20+,21+,23-,24-,25+/m1/s1
SMILES C[C@H](CO)[C@H]1CC[C@@]2(C)C3=C(CC[C@]12C)[C@@]1(C)CC[C@@H](C(C)(C)[C@@H]1CC3)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
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. callus n.a. PMID[10552648]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[18214349]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. seed n.a. PMID[21049975]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO8234 Vernonia galamensis Species Asteraceae Eukaryota n.a. seed n.a. PMID[9930408]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5540 Amorpha canescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8234 Vernonia galamensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8620 Caesalpinia major Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8009 Arctotis venusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8771 Heterodermia dissecta Species Physciaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4072 Anacyclus radiatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9455 Uncaria orientalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9455 Uncaria orientalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8620 Caesalpinia major Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5540 Amorpha canescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24536 Senecio cylindricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4875 Ugni molinae Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4072 Anacyclus radiatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9072 Bolocera tuediae Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8009 Arctotis venusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6292 Teucrium brevifolium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5832 Acacia nelsonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4321 Siphula ceratites Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8620 Caesalpinia major Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8234 Vernonia galamensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9330 Odinia antillensis Species Odiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2389 Pinus japonica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3668 Kalanchoe delagoensis Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8771 Heterodermia dissecta Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7188 Zieria granulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9455 Uncaria orientalis Species Rubiaceae 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

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 NPC108954 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
0.7647 Intermediate Similarity NPC73875
0.75 Intermediate Similarity NPC214570
0.7255 Intermediate Similarity NPC118508
0.7255 Intermediate Similarity NPC484086
0.7115 Intermediate Similarity NPC275910
0.7115 Intermediate Similarity NPC46160
0.7115 Intermediate Similarity NPC202642
0.6981 Remote Similarity NPC231477
0.6981 Remote Similarity NPC87489
0.6981 Remote Similarity NPC123724
0.6852 Remote Similarity NPC132635
0.6852 Remote Similarity NPC601223
0.6727 Remote Similarity NPC471724
0.6607 Remote Similarity NPC94755
0.6491 Remote Similarity NPC308041
0.6491 Remote Similarity NPC16350
0.6415 Remote Similarity NPC606082
0.6379 Remote Similarity NPC20388
0.6271 Remote Similarity NPC486193
0.6271 Remote Similarity NPC471720
0.6167 Remote Similarity NPC486187
0.5574 Remote Similarity NPC55309
0.5574 Remote Similarity NPC28252
0.55 Remote Similarity NPC171789
0.5484 Remote Similarity NPC233836
0.5484 Remote Similarity NPC159046
0.5484 Remote Similarity NPC469400
0.5484 Remote Similarity NPC187376
0.5238 Remote Similarity NPC484974
0.5238 Remote Similarity NPC23434
0.5156 Remote Similarity NPC76895
0.5156 Remote Similarity NPC486197
0.5152 Remote Similarity NPC474922
0.5079 Remote Similarity NPC471722
0.5079 Remote Similarity NPC605915
0.5077 Remote Similarity NPC482597

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC108954 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