Natural Product: NPC608257

Natural Product IDNPC608257
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KQIKOUUKQBTQBE-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL592005
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 KQIKOUUKQBTQBE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O7.ClH/c1-22-14-3-8(4-15(23-2)16(14)21)17-12(20)7-10-11(19)5-9(18)6-13(10)24-17;/h3-7H,1-2H3,(H3-,18,19,20,21);1H
SMILES COc1cc(-c2[o+]c3cc(O)cc(O)c3cc2O)cc(OC)c1O.[Cl-]

  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
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1104/pp.84.1.73]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12232319]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15286289]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. seed n.a. PMID[20947202]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22208890]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24253552]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Seeds n.a. n.a. PMID[28134521]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. whole plant n.a. PMID[28294414]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32415726]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37667613]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37917799]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38005226]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38067590]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39588261]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO61440 Vigna vexillata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23644 Clitoria ternatea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO60989 Canavalia ensiformis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Wax n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18321 Medicago sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23644 Clitoria ternatea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18321 Medicago sativa Species Fabaceae 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
NPT1592 Individual protein Dipeptidyl peptidase IV Homo sapiens IC50 = 1410.0 nM PMID[29609120]
NPT261 Individual protein Monoamine oxidase A Homo sapiens IC50 = 22100.0 nM PMID[29925480]

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 = 9000.0 nM PMID[28159411]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 9000.0 nM PMID[35932905]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 9000.0 nM PMID[28384544]
NPT28833 No target No relevant target n.a. Activity = 155.8 mg/L PMID[19944611]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 2.06 MU PMID[19944611]

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 NPC608257 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
0.9756 High Similarity NPC127624
0.7347 Intermediate Similarity NPC86655
0.6735 Remote Similarity NPC321979
0.6122 Remote Similarity NPC250432
0.5745 Remote Similarity NPC190454
0.5625 Remote Similarity NPC5447
0.551 Remote Similarity NPC46274
0.5263 Remote Similarity NPC202762

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608257 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
0.5625 Remote Similarity NPD1530 Clinical (unspecified phase)
0.551 Remote Similarity NPD1529 Clinical (unspecified phase)

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