Structure

Physi-Chem Properties

Molecular Weight:  190.1
Volume:  206.03
LogP:  3.337
LogD:  3.498
LogS:  -4.156
# Rotatable Bonds:  1
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.594
Synthetic Accessibility Score:  4.151
Fsp3:  0.417
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.462
MDCK Permeability:  2.2846188585390337e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.401
30% Bioavailability (F30%):  0.067

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.983
Plasma Protein Binding (PPB):  84.81291961669922%
Volume Distribution (VD):  0.529
Pgp-substrate:  11.953189849853516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.535
CYP1A2-substrate:  0.271
CYP2C19-inhibitor:  0.341
CYP2C19-substrate:  0.877
CYP2C9-inhibitor:  0.442
CYP2C9-substrate:  0.77
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.515
CYP3A4-inhibitor:  0.276
CYP3A4-substrate:  0.334

ADMET: Excretion

Clearance (CL):  4.71
Half-life (T1/2):  0.378

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.246
Drug-inuced Liver Injury (DILI):  0.238
AMES Toxicity:  0.686
Rat Oral Acute Toxicity:  0.732
Maximum Recommended Daily Dose:  0.675
Skin Sensitization:  0.95
Carcinogencity:  0.902
Eye Corrosion:  0.952
Eye Irritation:  0.971
Respiratory Toxicity:  0.961

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

  Natural Product: NPC490022

Natural Product ID:  NPC490022
Common Name*:   3-(2-Methylpropylidene)-3alpha,4-dihydro-1(3H)-isobenzofuranone
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IVZVUDRUEPCTTL-YRNVUSSQSA-N
Standard InCHI:  InChI=1S/C12H14O2/c1-8(2)7-11-9-5-3-4-6-10(9)12(13)14-11/h3-4,6-9H,5H2,1-2H3/b11-7+
SMILES:  CC(C)C=C1OC(=O)C2=CC=CCC12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0003408] Isobenzofurans

*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
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19778086]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Leaf Wax n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Pt n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26721 Apium graveolens Species Apiaceae 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
NPO26721 NPC490022 Raw Seed 81.65 13.3 150 mg/100g Database [DUKE]

☑ 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 NPC490022 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 NPC490022 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