Structure

Physi-Chem Properties

Molecular Weight:  177.99
Volume:  162.587
LogP:  2.302
LogD:  2.735
LogS:  -4.408
# Rotatable Bonds:  6
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.348
Synthetic Accessibility Score:  3.972
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.561
MDCK Permeability:  2.4714805476833135e-05
Pgp-inhibitor:  0.085
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.958
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.954
Plasma Protein Binding (PPB):  75.33446502685547%
Volume Distribution (VD):  0.977
Pgp-substrate:  4.251278400421143%

ADMET: Metabolism

CYP1A2-inhibitor:  0.899
CYP1A2-substrate:  0.887
CYP2C19-inhibitor:  0.975
CYP2C19-substrate:  0.834
CYP2C9-inhibitor:  0.884
CYP2C9-substrate:  0.888
CYP2D6-inhibitor:  0.502
CYP2D6-substrate:  0.906
CYP3A4-inhibitor:  0.694
CYP3A4-substrate:  0.4

ADMET: Excretion

Clearance (CL):  11.88
Half-life (T1/2):  0.237

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.89
Rat Oral Acute Toxicity:  0.581
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.964
Carcinogencity:  0.584
Eye Corrosion:  0.992
Eye Irritation:  0.995
Respiratory Toxicity:  0.962

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

  Natural Product: NPC220140

Natural Product ID:  NPC220140
Common Name*:   Allitridin
IUPAC Name:   3-(prop-2-enyltrisulfanyl)prop-1-ene
Synonyms:   Allitridin; Diallyl Trisulfide; Diallyltrisulfane; Diallyltrisulfide
Standard InCHIKey:  UBAXRAHSPKWNCX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H10S3/c1-3-5-7-9-8-6-4-2/h3-4H,1-2,5-6H2
SMILES:  C=CCSSSCC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL123040
PubChem CID:   16315
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0002799] Organic trisulfides

*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]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[26434122]
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 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 Shoot n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2055 Berberis integerrima Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
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]
NPO9952 Isoplexis sceptrum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2055 Berberis integerrima Species Berberidaceae 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]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4520 Allium macrostemon 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[TM-MC]
NPO8321 Allium chinense 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]
NPO8321 Allium chinense Species Amaryllidaceae 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]
NPO4520 Allium macrostemon Species Amaryllidaceae 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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3186 Loranthus parasiticus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9952 Isoplexis sceptrum Species Plantaginaceae 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

☑ 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
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat = 0.16 s-1 PMID[523271]
NPT1557 Individual Protein Glutathione reductase Homo sapiens Km = 160000.0 nM PMID[523271]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat/Km = 1000.0 M-1 s-1 PMID[523271]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat = 0.0011 s-1 PMID[523271]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 490.0 nM PMID[523272]
NPT53 Individual Protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 39810.7 nM PMID[523273]
NPT151 Individual Protein 15-hydroxyprostaglandin dehydrogenase [NAD+] Homo sapiens Potency = 28183.8 nM PMID[523273]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens Potency = 39810.7 nM PMID[523273]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 22387.2 nM PMID[523273]
NPT198 Individual Protein Vitamin D receptor Homo sapiens Potency n.a. 25118.9 nM PMID[523273]
NPT3141 Individual Protein Fatty acid synthase Gallus gallus IC50 = 8370.0 nM PMID[523275]
NPT616 Cell Line MDCK Canis lupus familiaris Activity = 33.1 % PMID[523276]
NPT616 Cell Line MDCK Canis lupus familiaris Activity = 38.6 % PMID[523276]
NPT616 Cell Line MDCK Canis lupus familiaris Activity = 34.6 % PMID[523276]
NPT616 Cell Line MDCK Canis lupus familiaris Activity = 26.8 % PMID[523276]
NPT616 Cell Line MDCK Canis lupus familiaris IC50 = 50000.0 nM PMID[523276]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 100000.0 nM PMID[523277]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 12589.3 nM PMID[523273]
NPT2 Others Unspecified Potency n.a. 5.1 nM PMID[523273]
NPT35 Others n.a. LogP = 2.98 n.a. PMID[523278]
NPT2 Others Unspecified Potency n.a. 29849.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 9439.2 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 NPC220140 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 NPC184203
0.9524 High Similarity NPC142438
0.8333 Intermediate Similarity NPC2088
0.8261 Intermediate Similarity NPC156018
0.8 Intermediate Similarity NPC46648
0.7143 Intermediate Similarity NPC204251
0.7143 Intermediate Similarity NPC168614
0.6364 Remote Similarity NPC239277
0.6087 Remote Similarity NPC33192
0.6087 Remote Similarity NPC254529
0.6061 Remote Similarity NPC277288
0.5833 Remote Similarity NPC476549
0.5833 Remote Similarity NPC225855
0.56 Remote Similarity NPC178306
0.56 Remote Similarity NPC476548
0.56 Remote Similarity NPC326758

  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 NPC220140 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