Natural Product: NPC606634

Natural Product IDNPC606634
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MRPDHXXPDCVBPQ-QEKTYAEASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1366071
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 MRPDHXXPDCVBPQ-QEKTYAEASA-N
Standard InCHI InChI=1S/C19H34O8/c1-10-7-12(21)8-18(3,4)19(10,25)6-5-11(2)26-17-16(24)15(23)14(22)13(9-20)27-17/h5-6,10-17,20-25H,7-9H2,1-4H3/b6-5+/t10-,11-,12+,13-,14-,15+,16-,17-,19-/m1/s1
SMILES C[C@H](/C=C/[C@@]1(O)[C@H](C)C[C@H](O)CC1(C)C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

  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
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. leaf n.a. DOI[10.1080/10412905.2001.9699624]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[11912066]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. leaf n.a. PMID[12419922]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. aerial part n.a. PMID[15577228]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. leaf n.a. PMID[21188975]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[21608987]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. PMID[22085682]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[30813368]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[38695450]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[38851735]
NPO60940 Turpenia ternata NAKAI n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO43281 Sadum sarmentosum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. Database[FooDB]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29515 Laurus nobilis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9246 Breynia officinalis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29515 Laurus nobilis Species Lauraceae 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
NPT484 Individual protein Luciferin 4-monooxygenase Photinus pyralis Potency n.a. 16944.1 nM PubChem BioAssay data set
NPT64 Individual protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 16353.5 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT28438 Unchecked Unchecked n.a. Potency = 730.8 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. Potency n.a. 1778.3 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. Potency n.a. 29092.9 nM PubChem BioAssay data set
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 11689.1 nM PubChem BioAssay data set

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 NPC606634 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
0.6207 Remote Similarity NPC154127
0.5593 Remote Similarity NPC169468
0.5593 Remote Similarity NPC81483
0.5593 Remote Similarity NPC214277
0.5593 Remote Similarity NPC307517
0.5593 Remote Similarity NPC61630
0.5439 Remote Similarity NPC312325
0.5085 Remote Similarity NPC25701
0.5085 Remote Similarity NPC2003

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC606634 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