Natural Product: NPC606450

Natural Product IDNPC606450
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PBFFEAJVASZNOS-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL221098
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 PBFFEAJVASZNOS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H24O6/c1-22-16-11-15(21)19(25-4)18(24-3)13(16)7-5-6-12-8-9-14(20)17(10-12)23-2/h8-11,20-21H,5-7H2,1-4H3
SMILES COc1cc(CCCc2c(OC)cc(O)c(OC)c2OC)ccc1O

  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
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[2082684]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[21922656]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3254039]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. aerial part n.a. PMID[3256207]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23218 Viscum coloratum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23218 Viscum coloratum Species Viscaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 17320.0 nM PMID[22197135]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 17800.0 nM PMID[22197135]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 14370.0 nM PMID[22197135]
NPT113 Cell line RAW264.7 Mus musculus Activity n.a. n.a. n.a. PMID[22197135]
NPT113 Cell line RAW264.7 Mus musculus Activity = 83.8 % PMID[22197135]
NPT34 Cell line BV-2 Mus musculus IC50 = 24000.0 nM PMID[17046255]
NPT113 Cell line RAW264.7 Mus musculus Activity = 70.6 % PMID[22197135]
NPT34 Cell line BV-2 Mus musculus IC50 = 29200.0 nM PMID[17046255]
NPT34 Cell line BV-2 Mus musculus Activity = 155.0 n.a. PMID[17046255]
NPT34 Cell line BV-2 Mus musculus Activity = 121.0 n.a. PMID[17046255]
NPT28438 Unchecked Unchecked n.a. Inhibition = 36.7 % PMID[17046255]
NPT28438 Unchecked Unchecked n.a. IC50 = 8300.0 nM PMID[17046255]
NPT28438 Unchecked Unchecked n.a. IC50 = 2500.0 nM PMID[17046255]
NPT28438 Unchecked Unchecked n.a. Inhibition = 53.5 % PMID[17046255]
NPT28438 Unchecked Unchecked n.a. IC50 = 12000.0 nM PMID[17046255]
NPT28438 Unchecked Unchecked n.a. IC50 = 1400.0 nM PMID[17046255]
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[22197135]
NPT28438 Unchecked Unchecked n.a. Activity = 67.0 n.a. PMID[17046255]
NPT28833 No target No relevant target n.a. IC50 = 49200.0 nM PMID[17046255]
NPT28438 Unchecked Unchecked n.a. Activity = 72.0 n.a. PMID[17046255]
NPT30106 Protein family cAMP-dependent protein kinase (PKA) Homo sapiens Inhibition n.a. n.a. % PMID[17046255]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 0.58 ug.mL-1 PMID[22197135]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 4.93 ug.mL-1 PMID[22197135]
NPT30135 Protein family Protein kinase C (PKC) Homo sapiens Inhibition = 34.4 % PMID[17046255]
NPT28859 Cell line CD4+ve Th n.a. Activity = 112.0 n.a. PMID[17046255]
NPT28859 Cell line CD4+ve Th n.a. Activity = 99.0 n.a. PMID[17046255]
NPT30135 Protein family Protein kinase C (PKC) Homo sapiens Inhibition = 48.8 % PMID[17046255]
NPT29326 Protein family Mitogen-activated protein kinase 1 and 3 (ERK2 and ERK1) Mus musculus Inhibition n.a. n.a. % PMID[22197135]
NPT21770 Protein family MAP kinase p38 Mus musculus Inhibition n.a. n.a. % PMID[22197135]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 4.98 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 3.92 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 4.28 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 63.6 % PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 76.2 % PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 3.46 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 4.08 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 8.64 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 11.54 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 2.45 U/mg PMID[22197135]
NPT32 Organism Mus musculus Mus musculus Activity = 10.97 U/mg PMID[22197135]





 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 NPC606450 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
0.7556 Intermediate Similarity NPC82679
0.6809 Remote Similarity NPC51840
0.6667 Remote Similarity NPC17943
0.6136 Remote Similarity NPC8547
0.6078 Remote Similarity NPC311680
0.5962 Remote Similarity NPC282000
0.5882 Remote Similarity NPC74817
0.5769 Remote Similarity NPC159968
0.5625 Remote Similarity NPC299406
0.5556 Remote Similarity NPC257124
0.5455 Remote Similarity NPC156840
0.54 Remote Similarity NPC177291
0.54 Remote Similarity NPC312675
0.54 Remote Similarity NPC262156
0.54 Remote Similarity NPC127937
0.54 Remote Similarity NPC184651
0.54 Remote Similarity NPC113865
0.5147 Remote Similarity NPC227902
0.5106 Remote Similarity NPC221049
0.5106 Remote Similarity NPC140359
0.5102 Remote Similarity NPC57490
0.5094 Remote Similarity NPC78974
0.5091 Remote Similarity NPC164386

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC606450 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
0.5556 Remote Similarity NPD228 Phase 0

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