Structure

Physi-Chem Properties

Molecular Weight:  204.12
Volume:  229.246
LogP:  3.949
LogD:  3.187
LogS:  -2.905
# Rotatable Bonds:  2
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.573
Synthetic Accessibility Score:  2.867
Fsp3:  0.231
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.782
MDCK Permeability:  2.364343890803866e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.345
Plasma Protein Binding (PPB):  97.44635772705078%
Volume Distribution (VD):  0.589
Pgp-substrate:  1.4244999885559082%

ADMET: Metabolism

CYP1A2-inhibitor:  0.912
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.093
CYP2C19-substrate:  0.644
CYP2C9-inhibitor:  0.119
CYP2C9-substrate:  0.764
CYP2D6-inhibitor:  0.431
CYP2D6-substrate:  0.893
CYP3A4-inhibitor:  0.056
CYP3A4-substrate:  0.302

ADMET: Excretion

Clearance (CL):  14.287
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.297
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.294
Rat Oral Acute Toxicity:  0.746
Maximum Recommended Daily Dose:  0.885
Skin Sensitization:  0.954
Carcinogencity:  0.592
Eye Corrosion:  0.271
Eye Irritation:  0.956
Respiratory Toxicity:  0.91

Download Data

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

  Natural Product: NPC109736

Natural Product ID:  NPC109736
Common Name*:   VBFJJMPOYIKNHB-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VBFJJMPOYIKNHB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H16O2/c1-8(2)5-6-11-7-12(14)9(3)10(4)13(11)15/h5,7H,6H2,1-4H3
SMILES:  CC(=CCC1=CC(=O)C(=C(C)C1=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10219885
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001534] Quinone and hydroquinone lipids
          • [CHEMONTID:0002802] Prenylquinones

*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
NPO23510 Vicia faba Species Fabaceae Eukaryota flowers n.a. n.a. PMID[16180811]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22014228]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. branch n.a. PMID[22014228]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22014228]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23747095]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31017 Polygonum orientale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25716 Persicaria orientalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31017 Polygonum orientale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25716 Persicaria orientalis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae 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

☑ 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 NPC109736 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 NPC109736 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