Structure

Physi-Chem Properties

Molecular Weight:  344.16
Volume:  345.099
LogP:  2.293
LogD:  1.949
LogS:  -4.534
# Rotatable Bonds:  1
TPSA:  69.04
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.577
Synthetic Accessibility Score:  5.416
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.229
MDCK Permeability:  1.7812419173424132e-05
Pgp-inhibitor:  0.597
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.331
30% Bioavailability (F30%):  0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.935
Plasma Protein Binding (PPB):  83.7350082397461%
Volume Distribution (VD):  1.932
Pgp-substrate:  16.510156631469727%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.724
CYP2C19-inhibitor:  0.493
CYP2C19-substrate:  0.77
CYP2C9-inhibitor:  0.36
CYP2C9-substrate:  0.06
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.359
CYP3A4-inhibitor:  0.69
CYP3A4-substrate:  0.468

ADMET: Excretion

Clearance (CL):  12.377
Half-life (T1/2):  0.731

ADMET: Toxicity

hERG Blockers:  0.073
Human Hepatotoxicity (H-HT):  0.663
Drug-inuced Liver Injury (DILI):  0.232
AMES Toxicity:  0.248
Rat Oral Acute Toxicity:  0.972
Maximum Recommended Daily Dose:  0.92
Skin Sensitization:  0.226
Carcinogencity:  0.907
Eye Corrosion:  0.146
Eye Irritation:  0.235
Respiratory Toxicity:  0.973

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC478471

Natural Product ID:  NPC478471
Common Name*:   VSWDORGPIHIGNW-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VSWDORGPIHIGNW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H9NS2/c7-5(8)6-3-1-2-4-6/h1-4H2,(H,7,8)
SMILES:  C1CCN(C1)C(=S)S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   65351
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[12444684]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[16441074]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO32963 Acremonium sp. Species Eukaryota n.a. Australian n.a. PMID[18288804]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[19053511]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[19199645]
NPO11959 Helminthostachys zeylanica Species Ophioglossaceae Eukaryota rhizomes n.a. n.a. PMID[19583252]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[22372956]
NPO32963 Acremonium sp. Species Eukaryota n.a. Mangrove Rhizophora apiculata n.a. PMID[22524636]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[22524636]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[25689430]
NPO32963 Acremonium sp. Species Eukaryota n.a. n.a. n.a. PMID[26928174]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[27588583]
NPO11959 Helminthostachys zeylanica Species Ophioglossaceae Eukaryota Rhizomes n.a. n.a. PMID[28169537]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[30724564]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11959 Helminthostachys zeylanica Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11959 Helminthostachys zeylanica Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11959 Helminthostachys zeylanica Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21178 Chloranthus serratus Species Chloranthaceae 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1886 Cell Line J774 Mus musculus Inhibition = 69.3 % PMID[17764147]
NPT1886 Cell Line J774 Mus musculus Inhibition = 42.2 % PMID[17764147]
NPT1886 Cell Line J774 Mus musculus Inhibition = 60.0 % PMID[17764147]
NPT1886 Cell Line J774 Mus musculus Inhibition = 63.9 % PMID[17764147]
NPT466 Cell Line U-937 Homo sapiens IC50 = 8.3 ug.mL-1 PMID[11374970]
NPT466 Cell Line U-937 Homo sapiens IC50 = 8.3 ug.mL-1 PMID[11908994]
NPT1886 Cell Line J774 Mus musculus Inhibition = 97.0 % PMID[21680063]
NPT3087 Individual Protein Transcription factor p65 Mus musculus Inhibition = 95.0 % PMID[21680063]
NPT369 Cell Line ACHN Homo sapiens GI50 = 230.0 nM PMID[25953156]
NPT82 Cell Line MDA-MB-231 Homo sapiens GI50 = 160.0 nM PMID[25953156]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 = 100.0 nM PMID[25953156]
NPT34 Cell Line BV-2 Mus musculus IC50 = 10800.0 nM PMID[28169537]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 66.5 % PMID[32371335]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 56.9 % PMID[32371335]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 0.125 ug.mL-1 PMID[17876006]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 16.0 ug.mL-1 PMID[17876006]
NPT19 Organism Escherichia coli Escherichia coli MIC = 64.0 ug.mL-1 PMID[17876006]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MBC = 0.5 ug ml-1 PMID[17876006]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis Activity = 0.5 ug ml-1 PMID[17876006]
NPT983 Protein Complex Nuclear factor NF-kappa-B complex Homo sapiens IC50 = 37200.0 nM PMID[24792464]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 130.0 nM PMID[25953156]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 140.0 nM PMID[25953156]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 170.0 nM PMID[25953156]
NPT983 Protein Complex Nuclear factor NF-kappa-B complex Homo sapiens IC50 = 34500.0 nM PMID[25953156]
NPT2 Others Unspecified IC50 = 37200.0 nM PMID[27096046]
NPT2 Others Unspecified IC50 = 37000.0 nM PMID[26928174]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC478471 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478471 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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