Natural Product: NPC606391

Natural Product IDNPC606391
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YIICVSCAKJMMDJ-SNVBAGLBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1456364
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004788] Diazanaphthalenes
        • [CHEMONTID:0004789] Benzodiazines
          • [CHEMONTID:0000485] Quinazolines

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 YIICVSCAKJMMDJ-SNVBAGLBSA-N
Standard InCHI InChI=1S/C11H12N2O/c14-10-5-6-13-7-8-3-1-2-4-9(8)12-11(10)13/h1-4,10,14H,5-7H2/t10-/m1/s1
SMILES O[C@@H]1CCN2Cc3ccccc3N=C12

  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
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[10757727]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota Seeds n.a. n.a. PMID[28128938]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[38971075]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[6736972]
NPO52241 Lunaria spp. Genus Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19021 Linaria vulgaris Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51920 Galega officinalis L. Genus Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25340 Galega officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44453 Anisotes sessiliflorus C.B.Cl. Genus Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31531 Adhatoda vasica n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19021 Linaria vulgaris Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25340 Galega officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31531 Adhatoda vasica n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO25340 Galega officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19021 Linaria vulgaris Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19021 Linaria vulgaris Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31531 Adhatoda vasica n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19021 Linaria vulgaris Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25340 Galega officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO568 Peganum nigellastrum Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15961 Sida cordifolia Species Malvaceae 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
NPT198 Individual protein Vitamin D receptor Homo sapiens Potency n.a. 3548.1 nM PubChem BioAssay data set
NPT442 Individual protein Ferritin light chain Equus caballus Potency = 35481.3 nM PubChem BioAssay data set
NPT53 Individual protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency n.a. 690.0 nM PubChem BioAssay data set
NPT53 Individual protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 2818.4 nM PubChem BioAssay data set
NPT53 Individual protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 2097.0 nM PubChem BioAssay data set
NPT443 Individual protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 5623.4 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT116 Cell line HL-60 Homo sapiens IC50 n.a. n.a. n.a. PMID[29229205]
NPT306 Cell line PC-3 Homo sapiens IC50 = 15410.0 nM PMID[29229205]
NPT515 Cell line SGC-7901 Homo sapiens IC50 n.a. n.a. n.a. PMID[29229205]

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 NPC606391 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 NPC328683
1.0 High Similarity NPC283130
0.58 Remote Similarity NPC164802
0.5577 Remote Similarity NPC608082

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC606391 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
1.0 High Similarity NPD478 Approved
0.58 Remote Similarity NPD477 Phase 1

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