Structure

Physi-Chem Properties

Molecular Weight:  129.02
Volume:  119.503
LogP:  1.269
LogD:  1.086
LogS:  -0.966
# Rotatable Bonds:  1
TPSA:  21.26
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.41
Synthetic Accessibility Score:  4.703
Fsp3:  0.4
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:  -4.573
MDCK Permeability:  2.090005909849424e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.138
30% Bioavailability (F30%):  0.174

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.936
Plasma Protein Binding (PPB):  57.57182312011719%
Volume Distribution (VD):  0.988
Pgp-substrate:  43.960174560546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.462
CYP1A2-substrate:  0.286
CYP2C19-inhibitor:  0.435
CYP2C19-substrate:  0.639
CYP2C9-inhibitor:  0.151
CYP2C9-substrate:  0.486
CYP2D6-inhibitor:  0.024
CYP2D6-substrate:  0.738
CYP3A4-inhibitor:  0.156
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  4.933
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.46
Drug-inuced Liver Injury (DILI):  0.407
AMES Toxicity:  0.894
Rat Oral Acute Toxicity:  0.395
Maximum Recommended Daily Dose:  0.862
Skin Sensitization:  0.171
Carcinogencity:  0.907
Eye Corrosion:  0.032
Eye Irritation:  0.591
Respiratory Toxicity:  0.713

Download Data

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

  Natural Product: NPC168129

Natural Product ID:  NPC168129
Common Name*:   R-5-Vinyl-2-Thiooxazolidone
IUPAC Name:   (5R)-5-ethenyl-1,3-oxazolidine-2-thione
Synonyms:  
Standard InCHIKey:  UZQVYLOFLQICCT-SCSAIBSYSA-N
Standard InCHI:  InChI=1S/C5H7NOS/c1-2-4-3-6-5(8)7-4/h2,4H,1,3H2,(H,6,8)/t4-/m1/s1
SMILES:  SC1=NC[C@H](O1)C=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL442589
PubChem CID:   3032313
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002491] Azolidines
        • [CHEMONTID:0000108] Oxazolidines

*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
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae 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
NPT2805 Individual Protein Dopamine beta-hydroxylase Bos taurus Activity = 62.0 nmol PMID[475851]
NPT364 Organism Lactuca sativa Lactuca sativa Activity > 40.0 % PMID[475852]

☑ 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 NPC168129 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 NPC43087
0.5682 Remote Similarity NPC27723

  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 NPC168129 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