Structure

Physi-Chem Properties

Molecular Weight:  166.05
Volume:  158.141
LogP:  2.273
LogD:  0.691
LogS:  -2.216
# Rotatable Bonds:  5
TPSA:  23.06
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.461
Synthetic Accessibility Score:  4.893
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:  -4.472
MDCK Permeability:  3.804398875217885e-05
Pgp-inhibitor:  0.016
Pgp-substrate:  0.647
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.884
Plasma Protein Binding (PPB):  81.9257583618164%
Volume Distribution (VD):  1.145
Pgp-substrate:  13.655814170837402%

ADMET: Metabolism

CYP1A2-inhibitor:  0.092
CYP1A2-substrate:  0.828
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.931
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.476
CYP2D6-inhibitor:  0.034
CYP2D6-substrate:  0.856
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.194

ADMET: Excretion

Clearance (CL):  10.941
Half-life (T1/2):  0.621

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.65
AMES Toxicity:  0.763
Rat Oral Acute Toxicity:  0.085
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.779
Carcinogencity:  0.698
Eye Corrosion:  0.989
Eye Irritation:  0.994
Respiratory Toxicity:  0.841

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  Natural Product: NPC326758

Natural Product ID:  NPC326758
Common Name*:   1-Propylsulfinylsulfanylpropane
IUPAC Name:   1-propylsulfinylsulfanylpropane
Synonyms:  
Standard InCHIKey:  XPRZAEWSYWTDSQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H14OS2/c1-3-5-8-9(7)6-4-2/h3-6H2,1-2H3
SMILES:  CCCSS(=O)CCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1224166
PubChem CID:   74761
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001161] Thiosulfinic acid esters

*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
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10388717]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10820136]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11695850]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1282214]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15102880]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15123652]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. urine n.a. PMID[15239850]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15466478]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16538977]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17499416]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18039809]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1814736]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1928373]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19572262]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19662622]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20951405]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2188748]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23384552]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23723388]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24085302]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24096206]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24343604]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24503197]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24814225]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25070706]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25727742]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26041992]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26485038]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26608498]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26654758]
NPO7191 Mimosa pudica Species Fabaceae Eukaryota n.a. root n.a. PMID[26661932]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26676627]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27466123]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3025936]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4002232]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[518564]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6273168]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6572072]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6806263]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6825837]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6833497]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[7311739]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[7645303]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8069858]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8452569]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9179722]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9435160]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9606952]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9629662]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9660093]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9694933]
NPO7191 Mimosa pudica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7191 Mimosa pudica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7191 Mimosa pudica Species Fabaceae 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
NPT214 Individual Protein Cathepsin B Homo sapiens Ki = 15600.0 nM PMID[476097]
NPT469 Individual Protein Cathepsin L Homo sapiens Ki = 11300.0 nM PMID[476097]
NPT469 Individual Protein Cathepsin L Homo sapiens TDI = 6664.0 /min/M PMID[476097]
NPT470 Individual Protein Rhodesain Trypanosoma brucei rhodesiense Ki = 4440.0 nM PMID[476097]
NPT470 Individual Protein Rhodesain Trypanosoma brucei rhodesiense TDI = 7150.0 /min/M PMID[476097]
NPT2 Others Unspecified Ki = 26400.0 nM PMID[476097]
NPT2 Others Unspecified TDI = 10761.0 /min/M PMID[476097]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 78300.0 nM PMID[476097]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 > 40000.0 nM PMID[476097]

☑ 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 NPC326758 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 NPC476548
0.9474 High Similarity NPC476549
0.9048 High Similarity NPC476550
0.76 Intermediate Similarity NPC46648
0.75 Intermediate Similarity NPC239277
0.72 Intermediate Similarity NPC2088
0.7143 Intermediate Similarity NPC254529
0.65 Remote Similarity NPC49871
0.65 Remote Similarity NPC264395
0.6364 Remote Similarity NPC266796
0.6207 Remote Similarity NPC168614
0.6207 Remote Similarity NPC204251
0.6 Remote Similarity NPC142438
0.5938 Remote Similarity NPC292366
0.5938 Remote Similarity NPC171713
0.5938 Remote Similarity NPC105023
0.5909 Remote Similarity NPC196982
0.5789 Remote Similarity NPC208362
0.56 Remote Similarity NPC220140
0.56 Remote Similarity NPC184203

  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 NPC326758 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
0.7083 Intermediate Similarity NPD8552 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD8550 Phase 3
0.6957 Remote Similarity NPD8229 Phase 3
0.68 Remote Similarity NPD8227 Approved
0.68 Remote Similarity NPD8230 Phase 3
0.6538 Remote Similarity NPD8551 Phase 3
0.6522 Remote Similarity NPD7375 Approved
0.6522 Remote Similarity NPD7377 Approved
0.6 Remote Similarity NPD7376 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