Structure

Physi-Chem Properties

Molecular Weight:  76.03
Volume:  78.953
LogP:  1.717
LogD:  1.32
LogS:  -1.26
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.413
Synthetic Accessibility Score:  2.74
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.63
MDCK Permeability:  0.0004684110463131219
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.828
Plasma Protein Binding (PPB):  87.1063232421875%
Volume Distribution (VD):  1.385
Pgp-substrate:  17.77635955810547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.692
CYP1A2-substrate:  0.505
CYP2C19-inhibitor:  0.052
CYP2C19-substrate:  0.895
CYP2C9-inhibitor:  0.024
CYP2C9-substrate:  0.44
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.354
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.258

ADMET: Excretion

Clearance (CL):  12.271
Half-life (T1/2):  0.767

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.401
Drug-inuced Liver Injury (DILI):  0.711
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.168
Maximum Recommended Daily Dose:  0.12
Skin Sensitization:  0.345
Carcinogencity:  0.563
Eye Corrosion:  0.842
Eye Irritation:  0.991
Respiratory Toxicity:  0.15

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  Natural Product: NPC264395

Natural Product ID:  NPC264395
Common Name*:   Propane-2-Thiol
IUPAC Name:   propane-2-thiol
Synonyms:  
Standard InCHIKey:  KJRCEJOSASVSRA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H8S/c1-3(2)4/h3-4H,1-2H3
SMILES:  CC(S)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1897156
PubChem CID:   6364
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0002485] Thiols
        • [CHEMONTID:0001212] Alkylthiols

*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
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. DOI[10.1007/s11306-014-0728-9]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
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]
NPO4934 Phaseolus vulgaris Species Fabaceae 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]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)89267-5]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf980687v]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1038/sdata.2014.29]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[11171227]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12576668]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[12882150]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15286289]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15666542]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[16748484]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons 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]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[20597533]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. seed n.a. PMID[20947202]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23656415]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24253552]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. seed n.a. PMID[25891114]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. trunk bark n.a. PMID[556731]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Tuber n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Wax n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Tubers n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. fruit n.a. Database[MetaboLights]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO667 Bulbus allii fistulosi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4934 Phaseolus vulgaris Species Fabaceae 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]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21080 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4934 Phaseolus vulgaris 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 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 44668.4 nM PMID[535967]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 33491.5 nM PMID[535967]
NPT102 Individual Protein Interleukin-8 Homo sapiens Potency n.a. 74978.0 nM PMID[535967]

☑ 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 NPC264395 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
1.0 High Similarity NPC49871
0.8235 Intermediate Similarity NPC266796
0.7647 Intermediate Similarity NPC239277
0.7222 Intermediate Similarity NPC254529
0.6842 Remote Similarity NPC476549
0.6667 Remote Similarity NPC196982
0.65 Remote Similarity NPC476548
0.65 Remote Similarity NPC326758
0.5909 Remote Similarity NPC476550
0.5909 Remote Similarity NPC142438

  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 NPC264395 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
NPD

  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