Structure

Physi-Chem Properties

Molecular Weight:  169.94
Volume:  125.924
LogP:  1.957
LogD:  3.014
LogS:  -2.278
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.512
Synthetic Accessibility Score:  5.134
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:  -5.775
MDCK Permeability:  4.862185051024426e-06
Pgp-inhibitor:  0.07
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.026

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.259
Plasma Protein Binding (PPB):  81.48482513427734%
Volume Distribution (VD):  1.298
Pgp-substrate:  5.660892009735107%

ADMET: Metabolism

CYP1A2-inhibitor:  0.995
CYP1A2-substrate:  0.411
CYP2C19-inhibitor:  0.882
CYP2C19-substrate:  0.783
CYP2C9-inhibitor:  0.642
CYP2C9-substrate:  0.825
CYP2D6-inhibitor:  0.197
CYP2D6-substrate:  0.844
CYP3A4-inhibitor:  0.731
CYP3A4-substrate:  0.726

ADMET: Excretion

Clearance (CL):  12.308
Half-life (T1/2):  0.814

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.076
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.885
Rat Oral Acute Toxicity:  0.93
Maximum Recommended Daily Dose:  0.055
Skin Sensitization:  0.973
Carcinogencity:  0.031
Eye Corrosion:  0.977
Eye Irritation:  0.996
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC110157

Natural Product ID:  NPC110157
Common Name*:   LCABDMYFXTZXMI-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LCABDMYFXTZXMI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H6S4/c1-4-2-6-7-3-5-1/h1-3H2
SMILES:  C1SCSSCS1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   520423
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001187] Thioacetals
        • [CHEMONTID:0002132] Dithioacetals

*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
NPO17824 Genipa americana Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[10425120]
NPO18632 Elfvingia applanata Species n.a. n.a. Fruits n.a. n.a. PMID[11975498]
NPO17824 Genipa americana Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[1667413]
NPO6984 Brickellia veronicaefolia Species Asteraceae Eukaryota essential oil n.a. n.a. PMID[16933870]
NPO695 Picea sitchensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17824 Genipa americana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12143 Corydalis solida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17824 Genipa americana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18300 Cyclamen persicum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO695 Picea sitchensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8183 Asplenium viviparum Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO254 Coreopsis capillacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6814 Pegaeophyton scapiflorum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2531 Daniellia oliveri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5089 Abies forrestii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6984 Brickellia veronicaefolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18632 Elfvingia applanata Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6636 Ophiorrhiza filistipula Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17824 Genipa americana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4093 Astragalus stipulosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18300 Cyclamen persicum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO695 Picea sitchensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1845 Physocarpus opulifolius Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3712 Pedicularis olgae Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12143 Corydalis solida Species Papaveraceae 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
NPT826 Organism Magnaporthe oryzae Magnaporthe oryzae MIC = 50.0 ug.mL-1 PMID[534674]

☑ 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 NPC110157 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

  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 NPC110157 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

  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