Structure

Physi-Chem Properties

Molecular Weight:  149.03
Volume:  134.495
LogP:  0.857
LogD:  1.326
LogS:  -2.469
# Rotatable Bonds:  1
TPSA:  3.24
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.518
Synthetic Accessibility Score:  3.438
Fsp3:  1.0
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:  -4.88
MDCK Permeability:  1.0480900527909398e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.559
Plasma Protein Binding (PPB):  10.78485107421875%
Volume Distribution (VD):  1.189
Pgp-substrate:  79.84648895263672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.091
CYP1A2-substrate:  0.367
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.951
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.295
CYP2D6-inhibitor:  0.312
CYP2D6-substrate:  0.919
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.554

ADMET: Excretion

Clearance (CL):  13.474
Half-life (T1/2):  0.462

ADMET: Toxicity

hERG Blockers:  0.074
Human Hepatotoxicity (H-HT):  0.273
Drug-inuced Liver Injury (DILI):  0.053
AMES Toxicity:  0.09
Rat Oral Acute Toxicity:  0.95
Maximum Recommended Daily Dose:  0.14
Skin Sensitization:  0.937
Carcinogencity:  0.268
Eye Corrosion:  0.995
Eye Irritation:  0.684
Respiratory Toxicity:  0.973

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

  Natural Product: NPC285308

Natural Product ID:  NPC285308
Common Name*:   Nereistoxin
IUPAC Name:   N,N-dimethyldithiolan-4-amine
Synonyms:  
Standard InCHIKey:  DSOOGBGKEWZRIH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H11NS2/c1-6(2)5-3-7-8-4-5/h5H,3-4H2,1-2H3/p+1
SMILES:  C[NH+](C)C1CSSC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2285758
PubChem CID:   15402
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000484] Dithiolanes
        • [CHEMONTID:0003372] 1,2-dithiolanes

*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
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24399 Lumbriconeis heteropoda n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24399 Lumbriconeis heteropoda n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae 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
NPT1304 Individual Protein Nicotinic acetylcholine receptor alpha 5 subunit Musca domestica Ki = 187000.0 nM PMID[448216]
NPT3925 Individual Protein Acetylcholine receptor protein alpha chain Torpedo californica IC50 = 953000.0 nM PMID[448217]
NPT3925 Individual Protein Acetylcholine receptor protein alpha chain Torpedo californica IC50 = 1068000.0 nM PMID[448217]
NPT350 Organism Tetranychus urticae Tetranychus urticae mortality = 30.0 % PMID[448214]
NPT21198 ORGANISM Chilo suppressalis Chilo suppressalis mortality = 100.0 % PMID[448214]
NPT1175 Organism Spodoptera litura Spodoptera litura mortality = 90.0 % PMID[448215]
NPT350 Organism Tetranychus urticae Tetranychus urticae mortality = 50.0 % PMID[448215]
NPT21200 ORGANISM Laodelphax striatella Laodelphax striatella mortality = 80.0 % PMID[448215]
NPT21198 ORGANISM Chilo suppressalis Chilo suppressalis mortality = 100.0 % PMID[448215]
NPT2 Others Unspecified Ki = 254000.0 nM PMID[448216]
NPT734 Organism Musca domestica Musca domestica LD50 = 0.49 ug PMID[448218]
NPT2 Others Unspecified IC50 = 228000.0 nM PMID[448218]
NPT2 Others Unspecified IC50 = 30700.0 nM PMID[448218]

☑ 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 NPC285308 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
0.7037 Intermediate Similarity NPC329501
0.6364 Remote Similarity NPC172064
0.6 Remote Similarity NPC266347

  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 NPC285308 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
0.5926 Remote Similarity NPD8816 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