Structure

Physi-Chem Properties

Molecular Weight:  90.05
Volume:  96.249
LogP:  2.017
LogD:  2.154
LogS:  -1.534
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.498
Synthetic Accessibility Score:  2.698
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:  -4.454
MDCK Permeability:  3.121174086118117e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.968
Plasma Protein Binding (PPB):  68.3165512084961%
Volume Distribution (VD):  1.747
Pgp-substrate:  46.758636474609375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.794
CYP1A2-substrate:  0.892
CYP2C19-inhibitor:  0.058
CYP2C19-substrate:  0.889
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.626
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.821
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.33

ADMET: Excretion

Clearance (CL):  11.247
Half-life (T1/2):  0.785

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.037
Drug-inuced Liver Injury (DILI):  0.641
AMES Toxicity:  0.023
Rat Oral Acute Toxicity:  0.074
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.24
Carcinogencity:  0.799
Eye Corrosion:  0.932
Eye Irritation:  0.991
Respiratory Toxicity:  0.07

Download Data

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

  Natural Product: NPC196982

Natural Product ID:  NPC196982
Common Name*:   Diethyl Sulfide
IUPAC Name:   ethylsulfanylethane
Synonyms:   Diethyl Sulfide; Ethylsulfanyl-Ethane
Standard InCHIKey:  LJSQFQKUNVCTIA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H10S/c1-3-5-4-2/h3-4H2,1-2H3
SMILES:  CCSCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL117181
PubChem CID:   9609
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001202] Thioethers
        • [CHEMONTID:0003862] Dialkylthioethers

*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
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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. 58128.9 nM PubChem BioAssay data set
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 65221.6 nM PubChem BioAssay data set
NPT162 Individual Protein Heat shock protein beta-1 Homo sapiens Potency n.a. 58128.9 nM PubChem BioAssay data set
NPT163 Individual Protein Nuclear factor NF-kappa-B p105 subunit Homo sapiens Potency n.a. 58128.9 nM PubChem BioAssay data set
NPT35 Others n.a. LogP = 1.95 n.a. PMID[453232]
NPT35 Others n.a. LogP = 1.9 n.a. PMID[453233]
NPT2 Others Unspecified Potency n.a. 163.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 65221.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 72514.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 58128.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 51807.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6462.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 51336 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 NPC196982 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
0.6842 Remote Similarity NPC239277
0.6667 Remote Similarity NPC49871
0.6667 Remote Similarity NPC264395
0.6522 Remote Similarity NPC156018
0.65 Remote Similarity NPC266796
0.65 Remote Similarity NPC254529
0.619 Remote Similarity NPC476549
0.5909 Remote Similarity NPC476548
0.5909 Remote Similarity NPC326758
0.5833 Remote Similarity NPC317406

  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 NPC196982 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