Natural Product: NPC471895

Natural Product IDNPC471895
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.
 2-Thiophenenecarboxaldehyde
IUPAC Name thiophene-2-carbaldehyde
Synonyms Thiophene-2-Carbaldehyde
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL328441
PubChem CID 7364
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000124] Aldehydes
            • [CHEMONTID:0003213] Aryl-aldehydes

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 CNUDBTRUORMMPA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C5H4OS/c6-4-5-2-1-3-7-5/h1-4H
SMILES C1=CSC(=C1)C=O

  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
NPO1099 Capparis spinosa Species Capparaceae Eukaryota aerial parts and buds Cagliari, Sardinia 2012-FEB PMID[22769561]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24014097]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24128451]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576 Brassica oleracea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7576 Brassica oleracea Species Brassicaceae 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
NPO7576 Brassica oleracea Other Stem 0.004 0.004 0.004 mg/100g Database [DUKE]

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
NPT200 Individual protein SARS coronavirus 3C-like proteinase SARS coronavirus Inhibition < 10.0 % PMID[21232949]
NPT813 Individual protein GABA transporter 1 Mus musculus Activity = 85.0 % PMID[31097402]
NPT813 Individual protein GABA transporter 1 Mus musculus Activity = 118.0 % PMID[30376325]
NPT591 Individual protein Glycogen synthase kinase-3 beta Homo sapiens IC50 > 100000.0 nM PMID[17938185]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT450 Organism Meloidogyne incognita Meloidogyne incognita EC50 = 14.08 ug.mL-1 PMID[23511021]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita EC50 = 105.0 ug.mL-1 PMID[7119809]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis IC50 n.a. n.a. n.a. PMID[34531949]
NPT1021 Organism Leishmania infantum Leishmania infantum IC50 > 100000.0 nM PMID[34531949]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis IC50 > 100000.0 nM PMID[34531949]
NPT29108 Cell line Peritoneal macrophage Mus musculus CC50 n.a. n.a. n.a. PMID[34531949]
NPT2 Others Unspecified n.a. IC50 > 4000000.0 nM PMID[22304344]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT450 Organism Meloidogyne incognita Meloidogyne incognita mortality = 100.0 % PMID[22769561]





 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 NPC471895 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 NPC217226
0.9 High Similarity NPC313823
0.6087 Remote Similarity NPC307163
0.6 Remote Similarity NPC148983
0.6 Remote Similarity NPC146316
0.5769 Remote Similarity NPC471376
0.5714 Remote Similarity NPC470794
0.5652 Remote Similarity NPC470796
0.56 Remote Similarity NPC146342
0.5455 Remote Similarity NPC231655
0.5217 Remote Similarity NPC156768
0.5217 Remote Similarity NPC219969

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471895 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
0.5455 Remote Similarity NPD9099 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