Structure

Physi-Chem Properties

Molecular Weight:  214.0
Volume:  186.368
LogP:  3.009
LogD:  3.439
LogS:  -5.218
# Rotatable Bonds:  7
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.452
Synthetic Accessibility Score:  3.461
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.521
MDCK Permeability:  2.5848170480458066e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.91
Plasma Protein Binding (PPB):  66.08438110351562%
Volume Distribution (VD):  1.142
Pgp-substrate:  15.35911750793457%

ADMET: Metabolism

CYP1A2-inhibitor:  0.813
CYP1A2-substrate:  0.928
CYP2C19-inhibitor:  0.988
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.884
CYP2C9-substrate:  0.88
CYP2D6-inhibitor:  0.083
CYP2D6-substrate:  0.758
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.197

ADMET: Excretion

Clearance (CL):  10.241
Half-life (T1/2):  0.083

ADMET: Toxicity

hERG Blockers:  0.241
Human Hepatotoxicity (H-HT):  0.101
Drug-inuced Liver Injury (DILI):  0.453
AMES Toxicity:  0.737
Rat Oral Acute Toxicity:  0.699
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.956
Carcinogencity:  0.29
Eye Corrosion:  0.984
Eye Irritation:  0.995
Respiratory Toxicity:  0.983

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

  Natural Product: NPC239277

Natural Product ID:  NPC239277
Common Name*:   Dipropyltetrasulfide
IUPAC Name:   1-(propyltetrasulfanyl)propane
Synonyms:   1,4-Dipropyltetrasulfane
Standard InCHIKey:  GJKGKILUTIBVOI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H14S4/c1-3-5-7-9-10-8-6-4-2/h3-6H2,1-2H3
SMILES:  CCCSSSSCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2030130
PubChem CID:   104285
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0003260] Sulfenyl compounds

*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
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.3923/pjbs.2013.1138.1144]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[17262437]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18326559]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Essential oil n.a. n.a. PMID[23163425]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23865201]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[24508058]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota garlic skin n.a. n.a. PMID[25726329]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7103 Allium sativum Species Amaryllidaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. MIC = 1.0 ug.mL-1 PMID[515258]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 32.0 ug.mL-1 PMID[515258]
NPT35 Others n.a. LogP = 3.45 n.a. PMID[515259]

☑ 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 NPC239277 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
0.8333 Intermediate Similarity NPC254529
0.7895 Intermediate Similarity NPC476549
0.7647 Intermediate Similarity NPC264395
0.7647 Intermediate Similarity NPC49871
0.75 Intermediate Similarity NPC476548
0.75 Intermediate Similarity NPC326758
0.7368 Intermediate Similarity NPC266796
0.6842 Remote Similarity NPC196982
0.6818 Remote Similarity NPC476550
0.6818 Remote Similarity NPC142438
0.6364 Remote Similarity NPC220140
0.6364 Remote Similarity NPC184203
0.5769 Remote Similarity NPC46648

  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 NPC239277 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
0.5833 Remote Similarity NPD8552 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8550 Phase 3

  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