Structure

Physi-Chem Properties

Molecular Weight:  170.02
Volume:  142.447
LogP:  -0.389
LogD:  -0.462
LogS:  0.625
# Rotatable Bonds:  4
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.518
Synthetic Accessibility Score:  3.346
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.365
MDCK Permeability:  2.5387067580595613e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.513
Plasma Protein Binding (PPB):  22.518991470336914%
Volume Distribution (VD):  0.614
Pgp-substrate:  65.2879409790039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.122
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.077
CYP2C19-substrate:  0.594
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.851
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.684
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.091

ADMET: Excretion

Clearance (CL):  3.599
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.078
Drug-inuced Liver Injury (DILI):  0.104
AMES Toxicity:  0.437
Rat Oral Acute Toxicity:  0.128
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.471
Carcinogencity:  0.743
Eye Corrosion:  0.974
Eye Irritation:  0.977
Respiratory Toxicity:  0.376

Download Data

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

  Natural Product: NPC327597

Natural Product ID:  NPC327597
Common Name*:   O,O-Diethyl S-Hydrogen Phosphorothioate
IUPAC Name:   diethoxy-hydroxy-sulfanylidene-$l^{5}-phosphane
Synonyms:  
Standard InCHIKey:  PKUWKAXTAVNIJR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H11O3PS/c1-3-6-8(5,9)7-4-2/h3-4H2,1-2H3,(H,5,9)
SMILES:  CCOP(=S)(O)OCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1232328
PubChem CID:   655
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001303] Organic thiophosphoric acids and derivatives
        • [CHEMONTID:0001572] Thiophosphoric acid esters
          • [CHEMONTID:0003383] Thiophosphate diesters

*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

☑ 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
NPT3044 Individual Protein Acetylcholinesterase Musca domestica IC50 > 25000000.0 nM PMID[566507]
NPT6180 Individual Protein Acetylcholinesterase Drosophila melanogaster IC50 > 40000000.0 nM PMID[566507]

☑ 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 NPC327597 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
0.6667 Remote Similarity NPC68114
0.6667 Remote Similarity NPC120097
0.6522 Remote Similarity NPC171090
0.5926 Remote Similarity NPC317545
0.5833 Remote Similarity NPC43196
0.5667 Remote Similarity NPC290971
0.56 Remote Similarity NPC294703

  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 NPC327597 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
0.8261 Intermediate Similarity NPD8559 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9038 Approved
0.6129 Remote Similarity NPD9679 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8547 Phase 2
0.5769 Remote Similarity NPD7385 Approved
0.5758 Remote Similarity NPD8612 Approved
0.5714 Remote Similarity NPD8220 Approved
0.5714 Remote Similarity NPD8219 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