Structure

Physi-Chem Properties

Molecular Weight:  161.96
Volume:  136.734
LogP:  3.035
LogD:  3.538
LogS:  -3.731
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.613
Synthetic Accessibility Score:  3.271
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.205
MDCK Permeability:  1.6597117792116478e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.043
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.845
Plasma Protein Binding (PPB):  74.31807708740234%
Volume Distribution (VD):  1.852
Pgp-substrate:  19.26187515258789%

ADMET: Metabolism

CYP1A2-inhibitor:  0.993
CYP1A2-substrate:  0.878
CYP2C19-inhibitor:  0.969
CYP2C19-substrate:  0.646
CYP2C9-inhibitor:  0.847
CYP2C9-substrate:  0.833
CYP2D6-inhibitor:  0.722
CYP2D6-substrate:  0.718
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.413

ADMET: Excretion

Clearance (CL):  11.899
Half-life (T1/2):  0.244

ADMET: Toxicity

hERG Blockers:  0.164
Human Hepatotoxicity (H-HT):  0.115
Drug-inuced Liver Injury (DILI):  0.844
AMES Toxicity:  0.856
Rat Oral Acute Toxicity:  0.244
Maximum Recommended Daily Dose:  0.08
Skin Sensitization:  0.946
Carcinogencity:  0.528
Eye Corrosion:  0.976
Eye Irritation:  0.995
Respiratory Toxicity:  0.986

Download Data

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

  Natural Product: NPC476214

Natural Product ID:  NPC476214
Common Name*:   2-(Methyldithio)Thiophene
IUPAC Name:   2-(methyldisulfanyl)thiophene
Synonyms:   2-(Methyldithio)Thiophene
Standard InCHIKey:  WRASPQWAKZMYQU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H6S3/c1-6-8-5-3-2-4-7-5/h2-4H,1H3
SMILES:  CSSC1=CC=CS1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL554538
PubChem CID:   45272211
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004144] Heteroaromatic 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
NPO13010 Allium stipitatum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[19093848]
NPO13010 Allium stipitatum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[19093848]
NPO13010 Allium stipitatum 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
NPT1176 Organism Mycobacterium fortuitum Mycobacterium fortuitum MIC > 128.0 ug.mL-1 PMID[482807]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 64.0 ug.mL-1 PMID[482807]
NPT1177 Organism Mycobacterium phlei Mycobacterium phlei MIC > 128.0 ug.mL-1 PMID[482807]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PMID[482807]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[482807]

☑ 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 NPC476214 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
0.92 High Similarity NPC108375
0.6912 Remote Similarity NPC105991
0.6479 Remote Similarity NPC327330
0.6338 Remote Similarity NPC470796
0.6184 Remote Similarity NPC8981
0.6104 Remote Similarity NPC195713
0.5875 Remote Similarity NPC307163
0.5823 Remote Similarity NPC471376
0.5753 Remote Similarity NPC470795
0.5679 Remote Similarity NPC471895
0.5641 Remote Similarity NPC299367

  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 NPC476214 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