Structure

Physi-Chem Properties

Molecular Weight:  192.08
Volume:  197.524
LogP:  2.671
LogD:  2.671
LogS:  -3.156
# Rotatable Bonds:  3
TPSA:  27.69
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  2.434
Fsp3:  0.273
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:  -4.466
MDCK Permeability:  3.487780486466363e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.055

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.464
Plasma Protein Binding (PPB):  91.74016571044922%
Volume Distribution (VD):  1.051
Pgp-substrate:  4.069586277008057%

ADMET: Metabolism

CYP1A2-inhibitor:  0.992
CYP1A2-substrate:  0.611
CYP2C19-inhibitor:  0.956
CYP2C19-substrate:  0.769
CYP2C9-inhibitor:  0.221
CYP2C9-substrate:  0.905
CYP2D6-inhibitor:  0.966
CYP2D6-substrate:  0.927
CYP3A4-inhibitor:  0.924
CYP3A4-substrate:  0.368

ADMET: Excretion

Clearance (CL):  13.551
Half-life (T1/2):  0.51

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.062
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.04
Skin Sensitization:  0.849
Carcinogencity:  0.956
Eye Corrosion:  0.08
Eye Irritation:  0.82
Respiratory Toxicity:  0.297

Download Data

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

  Natural Product: NPC152618

Natural Product ID:  NPC152618
Common Name*:   VGXJTTXSNPYTSK-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VGXJTTXSNPYTSK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H12O3/c1-3-4-8-5-6-9-11(10(8)12-2)14-7-13-9/h3,5-6H,1,4,7H2,2H3
SMILES:  C=CCc1ccc2c(c1OC)OCO2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5316141
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000296] Benzodioxoles

*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
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. PMID[15387676]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. seed n.a. PMID[21049973]
NPO16877 Aconitum episcopale Species Ranunculaceae Eukaryota n.a. root n.a. PMID[21417277]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[22365754]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[23701597]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[25819096]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[27329938]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[33296199]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468.2 Asarum heterotropoides f. schm. var. mandshuricum (maxim.) kitag. Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16552 Aromia moschata Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15902 Iris spuria Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7909 Parmelia vittata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15193 Cacia concinna n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9962 Pocillopora damicornis Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13926 Protaetia cuprea Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16877 Aconitum episcopale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3741 Pagrus major Species Sparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3939 Ardisia arborescens Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO29078 Asiasarum sieboldii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16119 Eucalyptus hybrid Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO745 Rubus trifidus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14126 Garcinia oligantha Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4659 Asiasarum heterotropoides n.a. n.a. n.a. 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

☑ 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 NPC152618 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 NPC152618 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