Structure

Physi-Chem Properties

Molecular Weight:  174.04
Volume:  160.679
LogP:  0.564
LogD:  0.668
LogS:  -0.823
# Rotatable Bonds:  2
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.663
Synthetic Accessibility Score:  4.101
Fsp3:  0.571
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:  -4.44
MDCK Permeability:  2.1732064851676114e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.119
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.965

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.995
Plasma Protein Binding (PPB):  74.36583709716797%
Volume Distribution (VD):  0.665
Pgp-substrate:  34.757320404052734%

ADMET: Metabolism

CYP1A2-inhibitor:  0.343
CYP1A2-substrate:  0.627
CYP2C19-inhibitor:  0.151
CYP2C19-substrate:  0.758
CYP2C9-inhibitor:  0.045
CYP2C9-substrate:  0.52
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.649
CYP3A4-inhibitor:  0.016
CYP3A4-substrate:  0.2

ADMET: Excretion

Clearance (CL):  7.736
Half-life (T1/2):  0.915

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.907
Drug-inuced Liver Injury (DILI):  0.879
AMES Toxicity:  0.242
Rat Oral Acute Toxicity:  0.122
Maximum Recommended Daily Dose:  0.792
Skin Sensitization:  0.949
Carcinogencity:  0.869
Eye Corrosion:  0.011
Eye Irritation:  0.581
Respiratory Toxicity:  0.17

Download Data

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

  Natural Product: NPC317548

Natural Product ID:  NPC317548
Common Name*:   Thiopalmyrone
IUPAC Name:   (2R)-2-(hydroxymethyl)-4-methoxy-2,3-dihydrothiopyran-6-one
Synonyms:   Thiopalmyrone
Standard InCHIKey:  LDZGBXIHQQUFKM-ZCFIWIBFSA-N
Standard InCHI:  InChI=1S/C7H10O3S/c1-10-5-2-6(4-8)11-7(9)3-5/h3,6,8H,2,4H2,1H3/t6-/m1/s1
SMILES:  OC[C@H]1CC(=CC(=O)S1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1782852
PubChem CID:   53355799
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001895] Thiopyrans

*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
NPO31273 Oscillatoria sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[16930043]
NPO31273 Oscillatoria sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17328572]
NPO31273 Oscillatoria sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20525864]
NPO29939 Hormoscilla Genus Gomontiellaceae Bacteria n.a. n.a. n.a. PMID[21473610]
NPO31273 Oscillatoria sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21473610]
NPO31273 Oscillatoria sp. Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21999614]

☑ 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
NPT3469 Organism Biomphalaria glabrata Biomphalaria glabrata LC50 = 8300.0 nM PMID[546586]

☑ 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 NPC317548 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
0.65 Remote Similarity NPC477779
0.6333 Remote Similarity NPC477777
0.6316 Remote Similarity NPC158853
0.625 Remote Similarity NPC66365
0.6207 Remote Similarity NPC477776
0.6184 Remote Similarity NPC55732
0.5902 Remote Similarity NPC288381
0.5902 Remote Similarity NPC20934
0.5902 Remote Similarity NPC225974
0.5873 Remote Similarity NPC116366
0.5645 Remote Similarity NPC220191
0.5645 Remote Similarity NPC107703
0.5616 Remote Similarity NPC134593

  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 NPC317548 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
0.6316 Remote Similarity NPD9090 Phase 3
0.5789 Remote Similarity NPD9091 Suspended
0.5789 Remote Similarity NPD9297 Discontinued
0.5781 Remote Similarity NPD539 Approved

  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