Structure

Physi-Chem Properties

Molecular Weight:  152.03
Volume:  140.845
LogP:  1.666
LogD:  0.343
LogS:  -1.583
# Rotatable Bonds:  4
TPSA:  23.06
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.453
Synthetic Accessibility Score:  4.866
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:  -4.59
MDCK Permeability:  3.534154166118242e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.657
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.911
Plasma Protein Binding (PPB):  66.13482666015625%
Volume Distribution (VD):  1.121
Pgp-substrate:  27.54436683654785%

ADMET: Metabolism

CYP1A2-inhibitor:  0.064
CYP1A2-substrate:  0.766
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.915
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.304
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.73
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.249

ADMET: Excretion

Clearance (CL):  9.876
Half-life (T1/2):  0.583

ADMET: Toxicity

hERG Blockers:  0.062
Human Hepatotoxicity (H-HT):  0.078
Drug-inuced Liver Injury (DILI):  0.537
AMES Toxicity:  0.457
Rat Oral Acute Toxicity:  0.224
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.912
Carcinogencity:  0.717
Eye Corrosion:  0.991
Eye Irritation:  0.994
Respiratory Toxicity:  0.953

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

  Natural Product: NPC476548

Natural Product ID:  NPC476548
Common Name*:   Butyl(methylthio) sulfoxide
IUPAC Name:   1-methylsulfanylsulfinylbutane
Synonyms:   S-Methyl N-Butanethiosulfinate
Standard InCHIKey:  FHZCERVLGUGKEY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H12OS2/c1-3-4-5-8(6)7-2/h3-5H2,1-2H3
SMILES:  CCCCS(=O)SC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10012106
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
NPO8374 Allium siculum Species Amaryllidaceae Eukaryota bulb n.a. n.a. PMID[12141853]
NPO8374 Allium siculum 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
NPT314 Organism Bacillus cereus Bacillus cereus IZ = 0 mm PMID[12141853]
NPT314 Organism Bacillus cereus Bacillus cereus IZ = 30 mm PMID[12141853]
NPT314 Organism Bacillus cereus Bacillus cereus IZ = 34 mm PMID[12141853]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 8 mm PMID[12141853]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 30 mm PMID[12141853]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 38 mm PMID[12141853]
NPT2710 Organism Streptococcus agalactiae Streptococcus agalactiae IZ = 0 mm PMID[12141853]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0 mm PMID[12141853]
NPT19 Organism Escherichia coli Escherichia coli IZ = 22 mm PMID[12141853]
NPT19 Organism Escherichia coli Escherichia coli IZ = 24 mm PMID[12141853]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 0 mm PMID[12141853]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 8 mm PMID[12141853]
NPT1521 Organism Stenotrophomonas maltophilia Stenotrophomonas maltophilia IZ = 0 mm PMID[12141853]
NPT1521 Organism Stenotrophomonas maltophilia Stenotrophomonas maltophilia IZ = 12 mm PMID[12141853]
NPT1521 Organism Stenotrophomonas maltophilia Stenotrophomonas maltophilia IZ = 14 mm PMID[12141853]
NPT2923 Organism Klebsiella pneumoniae subsp. pneumoniae Klebsiella pneumoniae subsp. pneumoniae IZ = 0 mm PMID[12141853]
NPT2923 Organism Klebsiella pneumoniae subsp. pneumoniae Klebsiella pneumoniae subsp. pneumoniae IZ = 16 mm PMID[12141853]
NPT2923 Organism Klebsiella pneumoniae subsp. pneumoniae Klebsiella pneumoniae subsp. pneumoniae IZ = 18 mm PMID[12141853]

☑ 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 NPC476548 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 NPC326758
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 NPC264395
0.65 Remote Similarity NPC49871
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 NPC476548 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