Natural Product: NPC260218

Natural Product IDNPC260218
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DNVPQKQSNYMLRS-GTJXICOESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 124928616
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003567] Ergostane steroids
          • [CHEMONTID:0001403] Ergosterols and derivatives

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 DNVPQKQSNYMLRS-GTJXICOESA-N
Standard InCHI InChI=1S/C28H44O/c1-18(2)19(3)7-8-20(4)24-11-12-25-23-10-9-21-17-22(29)13-15-27(21,5)26(23)14-16-28(24,25)6/h7-10,18-20,22,24-26,29H,11-17H2,1-6H3/b8-7+/t19-,20-,22-,24+,25+,26+,27-,28+/m0/s1
SMILES CC(C)[C@@H](C)/C=C/[C@H](C)[C@H]1CC[C@@H]2C3=CC=C4C[C@H](CC[C@]4(C)[C@@H]3CC[C@]12C)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
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. n.a. n.a. PMID[10075800]
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. n.a. n.a. PMID[10650102]
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. Mandapam Coast, Tamilnadu, India n.a. PMID[22704923]
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. n.a. n.a. PMID[9463111]
NPO17210 Dorstenia barnimiana Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16684 Alibertia macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13746 Achillea leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13985 Oxybasis urbica Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9044 Rubia ustulata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17991 Sedum forsterianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16323 Umbilicaria proboscidea Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1793 Uvaria mocoli Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7857 Verbascum georgicum Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13321 Viguiera cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16204 Zieria chevalieri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13746 Achillea leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16323 Umbilicaria proboscidea Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13746 Achillea leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16684 Alibertia macrophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16323 Umbilicaria proboscidea Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17673 Dysidea herbacea Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13746 Achillea leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13321 Viguiera cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1793 Uvaria mocoli Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17210 Dorstenia barnimiana Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9044 Rubia ustulata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13985 Oxybasis urbica Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16204 Zieria chevalieri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17991 Sedum forsterianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7857 Verbascum georgicum Species Scrophulariaceae 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 NPC260218 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
1.0 High Similarity NPC307965
1.0 High Similarity NPC18603
1.0 High Similarity NPC491013
0.7115 Intermediate Similarity NPC183927
0.5789 Remote Similarity NPC204188
0.5789 Remote Similarity NPC80561
0.5789 Remote Similarity NPC329596
0.5758 Remote Similarity NPC267510
0.5714 Remote Similarity NPC134330
0.5614 Remote Similarity NPC611620
0.5345 Remote Similarity NPC154330
0.5333 Remote Similarity NPC49422
0.5333 Remote Similarity NPC9161
0.5312 Remote Similarity NPC472220
0.5312 Remote Similarity NPC97884
0.5254 Remote Similarity NPC129165
0.5254 Remote Similarity NPC113733
0.5246 Remote Similarity NPC291484
0.5167 Remote Similarity NPC234193
0.5079 Remote Similarity NPC118648
0.5079 Remote Similarity NPC475022
0.5079 Remote Similarity NPC600021

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC260218 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
0.5614 Remote Similarity NPD7150 Approved
0.5614 Remote Similarity NPD7151 Phase 4
0.5614 Remote Similarity NPD7152 Approved
0.5333 Remote Similarity NPD7143 Approved
0.5333 Remote Similarity NPD7144 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