Natural Product: NPC608742

Natural Product IDNPC608742
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZWVNKIJIVBIMSW-SXFAUFNYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4860522
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0002934] Flavonoid O-glucuronides
              • [CHEMONTID:0003534] Flavonoid-7-O-glucuronides

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 ZWVNKIJIVBIMSW-SXFAUFNYSA-N
Standard InCHI InChI=1S/C22H20O11/c1-30-10-4-2-9(3-5-10)14-8-13(24)16-12(23)6-11(7-15(16)32-14)31-22-19(27)17(25)18(26)20(33-22)21(28)29/h2-8,17-20,22-23,25-27H,1H3,(H,28,29)/t17-,18-,19+,20-,22+/m0/s1
SMILES COc1ccc(-c2cc(=O)c3c(O)cc(O[C@@H]4O[C@H](C(=O)O)[C@@H](O)[C@H](O)[C@H]4O)cc3o2)cc1

  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
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22060189]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. fruit n.a. PMID[22396124]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. flower n.a. PMID[22723874]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23371463]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flowers Lasa, China n.a. PMID[24621197]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27748595]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39732883]
NPO21215 Tripora divaricata n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Bud n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21215 Tripora divaricata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9064 Cirsium arvense Species Asteraceae 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 = 92400.0 nM PMID[33667099]
NPT113 Cell line RAW264.7 Mus musculus CC50 > 100000.0 nM PMID[33667099]

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 NPC608742 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
0.8514 High Similarity NPC282169
0.8267 Intermediate Similarity NPC20505
0.6897 Remote Similarity NPC46202
0.675 Remote Similarity NPC95090
0.675 Remote Similarity NPC27408
0.6707 Remote Similarity NPC237435
0.6667 Remote Similarity NPC181712
0.6627 Remote Similarity NPC43211
0.6588 Remote Similarity NPC600989
0.6286 Remote Similarity NPC29353
0.6277 Remote Similarity NPC253685
0.619 Remote Similarity NPC101191
0.6118 Remote Similarity NPC210094
0.6064 Remote Similarity NPC479765
0.6047 Remote Similarity NPC115760
0.6047 Remote Similarity NPC610187
0.6022 Remote Similarity NPC229409
0.5978 Remote Similarity NPC64051
0.5957 Remote Similarity NPC479766
0.5934 Remote Similarity NPC22062
0.5934 Remote Similarity NPC473634
0.5934 Remote Similarity NPC138811
0.593 Remote Similarity NPC135277
0.5862 Remote Similarity NPC22832
0.5862 Remote Similarity NPC243930
0.5814 Remote Similarity NPC27942
0.5795 Remote Similarity NPC220169
0.5714 Remote Similarity NPC331652
0.5684 Remote Similarity NPC473623
0.5682 Remote Similarity NPC80188
0.5647 Remote Similarity NPC39360
0.5647 Remote Similarity NPC19709
0.5647 Remote Similarity NPC29763
0.5647 Remote Similarity NPC210003
0.5625 Remote Similarity NPC488089
0.5618 Remote Similarity NPC607707
0.5581 Remote Similarity NPC189142
0.5581 Remote Similarity NPC77660
0.5567 Remote Similarity NPC475382
0.5529 Remote Similarity NPC473043
0.5506 Remote Similarity NPC264735
0.5444 Remote Similarity NPC311830
0.5405 Remote Similarity NPC127447
0.5385 Remote Similarity NPC190003
0.5341 Remote Similarity NPC186807
0.5333 Remote Similarity NPC234133
0.5333 Remote Similarity NPC601144
0.5325 Remote Similarity NPC195202
0.5325 Remote Similarity NPC223579
0.5287 Remote Similarity NPC58053
0.5287 Remote Similarity NPC261866
0.5263 Remote Similarity NPC108406
0.5222 Remote Similarity NPC235260
0.5222 Remote Similarity NPC155763
0.5204 Remote Similarity NPC209296
0.5196 Remote Similarity NPC11468
0.5176 Remote Similarity NPC248739
0.5161 Remote Similarity NPC211594
0.5132 Remote Similarity NPC33265
0.5132 Remote Similarity NPC48479
0.5132 Remote Similarity NPC57030
0.5111 Remote Similarity NPC138927
0.5106 Remote Similarity NPC606546
0.5057 Remote Similarity NPC158027
0.5056 Remote Similarity NPC18699
0.5055 Remote Similarity NPC49344

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608742 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
0.6707 Remote Similarity NPD4338 Clinical (unspecified phase)
0.5204 Remote Similarity NPD7054 Phase 4

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