Structure

Physi-Chem Properties

Molecular Weight:  148.04
Volume:  146.714
LogP:  2.823
LogD:  3.106
LogS:  -3.683
# Rotatable Bonds:  5
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.334
Synthetic Accessibility Score:  3.378
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.346
MDCK Permeability:  2.8536453100969084e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.438
30% Bioavailability (F30%):  0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.898
Plasma Protein Binding (PPB):  76.42951202392578%
Volume Distribution (VD):  1.226
Pgp-substrate:  6.192480564117432%

ADMET: Metabolism

CYP1A2-inhibitor:  0.888
CYP1A2-substrate:  0.908
CYP2C19-inhibitor:  0.733
CYP2C19-substrate:  0.888
CYP2C9-inhibitor:  0.138
CYP2C9-substrate:  0.831
CYP2D6-inhibitor:  0.116
CYP2D6-substrate:  0.914
CYP3A4-inhibitor:  0.224
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  13.746
Half-life (T1/2):  0.38

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.023
Drug-inuced Liver Injury (DILI):  0.042
AMES Toxicity:  0.416
Rat Oral Acute Toxicity:  0.069
Maximum Recommended Daily Dose:  0.032
Skin Sensitization:  0.943
Carcinogencity:  0.538
Eye Corrosion:  0.989
Eye Irritation:  0.996
Respiratory Toxicity:  0.469

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC142438

Natural Product ID:  NPC142438
Common Name*:   1-(Prop-2-Enyldisulfanyl)Propane
IUPAC Name:   1-(prop-2-enyldisulfanyl)propane
Synonyms:  
Standard InCHIKey:  FCSSPCOFDUKHPV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12S2/c1-3-5-7-8-6-4-2/h3H,1,4-6H2,2H3
SMILES:  CCCSSCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187351
PubChem CID:   16591
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0004195] Allyl sulfur 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]
NPO10434 Rhodospirillum rubrum Species Rhodospirillaceae Bacteria n.a. n.a. n.a. PMID[18826254]
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]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. PMID[24467533]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. fruit n.a. PMID[24467533]
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]
NPO13017 Nauclea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[31429278]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
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 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 n.a. n.a. n.a. Database[HerDing]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2055 Berberis integerrima Species Berberidaceae 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]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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]
NPO11481 Elephantopus angustifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8817 Herbertus sakuraii Species Herbertaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10434 Rhodospirillum rubrum Species Rhodospirillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4177 Libocedrus decurrens Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8146 Aniba megaphylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13017 Nauclea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1625 Ovibos moschatus Species Bovidae 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
NPO7103 NPC142438 Raw Bulb 12.6 3.6 21.6 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified Potency n.a. 435 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 60944.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 683.8 nM PubChem BioAssay data set

☑ 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 NPC142438 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
0.9524 High Similarity NPC184203
0.9524 High Similarity NPC220140
0.84 Intermediate Similarity NPC46648
0.8 Intermediate Similarity NPC2088
0.7917 Intermediate Similarity NPC156018
0.6897 Remote Similarity NPC168614
0.6897 Remote Similarity NPC204251
0.6818 Remote Similarity NPC239277
0.6522 Remote Similarity NPC254529
0.6364 Remote Similarity NPC277288
0.625 Remote Similarity NPC476549
0.625 Remote Similarity NPC225855
0.6 Remote Similarity NPC326758
0.6 Remote Similarity NPC476548
0.6 Remote Similarity NPC178306
0.5909 Remote Similarity NPC264395
0.5909 Remote Similarity NPC49871
0.5833 Remote Similarity NPC205586
0.5833 Remote Similarity NPC266796
0.5833 Remote Similarity NPC33192
0.5769 Remote Similarity NPC96619

  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 NPC142438 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