Natural Product: NPC45603

Natural Product IDNPC45603
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YAXRKAKOIWXVHL-KGJRQOPQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001691] Steroid esters

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 YAXRKAKOIWXVHL-KGJRQOPQSA-N
Standard InCHI InChI=1S/C30H48O2/c1-19(2)20(3)8-9-21(4)26-12-13-27-25-11-10-23-18-24(32-22(5)31)14-16-29(23,6)28(25)15-17-30(26,27)7/h8-10,19-21,24-28H,11-18H2,1-7H3/b9-8+/t20-,21-,24-,25+,26+,27+,28+,29-,30+/m0/s1
SMILES CC(C)[C@@H](C)/C=C/[C@H](C)[C@H]1CC[C@@H]2[C@H]3CC=C4C[C@H](CC[C@]4(C)[C@@H]3CC[C@]12C)OC(=O)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
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[22281186]
NPO21305 Carpesium macrocephalum Species Asteraceae Eukaryota Whole Plant n.a. n.a. PMID[26394911]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[27588326]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[29338260]
NPO21305 Carpesium macrocephalum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39407585]
NPO22452 Leucanthemum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22452 Leucanthemum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22452 Leucanthemum vulgare Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21305 Carpesium macrocephalum 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

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 NPC45603 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
0.7636 Intermediate Similarity NPC44083
0.7455 Intermediate Similarity NPC153987
0.6727 Remote Similarity NPC609635
0.5821 Remote Similarity NPC264127
0.5821 Remote Similarity NPC470613
0.5821 Remote Similarity NPC470612
0.5797 Remote Similarity NPC158088
0.5735 Remote Similarity NPC469599
0.5652 Remote Similarity NPC154452
0.5652 Remote Similarity NPC121072
0.5652 Remote Similarity NPC100451
0.5593 Remote Similarity NPC154330
0.5574 Remote Similarity NPC75810
0.5571 Remote Similarity NPC21064
0.5571 Remote Similarity NPC485606
0.55 Remote Similarity NPC113733
0.5484 Remote Similarity NPC33913
0.5294 Remote Similarity NPC207617
0.5294 Remote Similarity NPC607440
0.5238 Remote Similarity NPC474207
0.5125 Remote Similarity NPC272015
0.5079 Remote Similarity NPC93027
0.5075 Remote Similarity NPC472220
0.5075 Remote Similarity NPC97884

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC45603 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
0.5938 Remote Similarity NPD6399 Phase 3
0.5068 Remote Similarity NPD6635 Phase 4

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