Natural Product: NPC608751

Natural Product IDNPC608751
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HRSGCYGUWHGOPY-LYHHMGRNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2269162
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids 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 HRSGCYGUWHGOPY-LYHHMGRNSA-N
Standard InCHI InChI=1S/C20H31NO7/c1-6-12(2)17(23)28-15-8-10-21-9-7-14(16(15)21)11-27-18(24)20(26,13(3)22)19(4,5)25/h6-7,13,15-16,22,25-26H,8-11H2,1-5H3/b12-6-/t13-,15+,16+,20-/m0/s1
SMILES C/C=C(/C)C(=O)O[C@@H]1CCN2CC=C(COC(=O)[C@@](O)([C@H](C)O)C(C)(C)O)[C@H]12

  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
NPO21144 Symphytum orientale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9866 Symphytum tuberosum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47550 Symphytum tuberosum L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52568 Symphytum officinale L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44484 Symphytum bulbosum K. F. Schimp. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53088 Symphytum asperum Lepech. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52178 Echium vulgare L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7000 Echium italicum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23223 Symphytum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO54651 Echium lycopsis Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58000 Echium setosum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55539 Symphytum caucasium Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21144 Symphytum orientale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23223 Symphytum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9866 Symphytum tuberosum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23223 Symphytum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21144 Symphytum orientale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9866 Symphytum tuberosum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23223 Symphytum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21144 Symphytum orientale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21144 Symphytum orientale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23223 Symphytum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7000 Echium italicum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9866 Symphytum tuberosum Species Boraginaceae 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
NPT1161 Cell line CHO Cricetulus griseus EC50 n.a. n.a. n.a. DOI[10.1016/jbse.2007.08.015]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 165.0 % DOI[10.1016/jbse.2007.08.015]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis EC50 > 50.0 microg/cm2 DOI[10.1016/jbse.2007.08.015]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 118.0 % DOI[10.1016/jbse.2007.08.015]
NPT1275 Organism Leptinotarsa decemlineata Leptinotarsa decemlineata EC50 = 1.4 microg/cm2 DOI[10.1016/jbse.2007.08.015]
NPT2528 Organism Rhopalosiphum padi Rhopalosiphum padi Activity = 36.0 % DOI[10.1016/jbse.2007.08.015]
NPT348 Organism Myzus persicae Myzus persicae Activity = 40.0 % DOI[10.1016/jbse.2007.08.015]

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 NPC608751 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
0.8103 Intermediate Similarity NPC609037
0.7377 Intermediate Similarity NPC608959
0.7167 Intermediate Similarity NPC130124
0.7167 Intermediate Similarity NPC193471
0.6935 Remote Similarity NPC47857
0.6935 Remote Similarity NPC181510
0.6935 Remote Similarity NPC168758
0.6935 Remote Similarity NPC602310
0.6885 Remote Similarity NPC608663
0.6825 Remote Similarity NPC201889
0.6825 Remote Similarity NPC106791
0.6825 Remote Similarity NPC607716
0.6452 Remote Similarity NPC30911
0.6452 Remote Similarity NPC608092
0.6308 Remote Similarity NPC23963
0.6061 Remote Similarity NPC316984
0.5797 Remote Similarity NPC600980
0.5522 Remote Similarity NPC609380
0.5147 Remote Similarity NPC610562

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608751 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
0.6452 Remote Similarity NPD2204 Approved

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