Structure

Physi-Chem Properties

Molecular Weight:  236.07
Volume:  229.764
LogP:  1.114
LogD:  1.043
LogS:  -2.359
# Rotatable Bonds:  2
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.821
Synthetic Accessibility Score:  2.557
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.878
MDCK Permeability:  9.253544703824446e-06
Pgp-inhibitor:  0.002
Pgp-substrate:  0.888
Human Intestinal Absorption (HIA):  0.037
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.922

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.073
Plasma Protein Binding (PPB):  73.64762878417969%
Volume Distribution (VD):  0.885
Pgp-substrate:  30.543237686157227%

ADMET: Metabolism

CYP1A2-inhibitor:  0.912
CYP1A2-substrate:  0.963
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.698
CYP2C9-inhibitor:  0.044
CYP2C9-substrate:  0.702
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.714
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.359

ADMET: Excretion

Clearance (CL):  7.137
Half-life (T1/2):  0.915

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.44
AMES Toxicity:  0.478
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.071
Skin Sensitization:  0.374
Carcinogencity:  0.043
Eye Corrosion:  0.003
Eye Irritation:  0.299
Respiratory Toxicity:  0.15

Download Data

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

  Natural Product: NPC276384

Natural Product ID:  NPC276384
Common Name*:   NDYIQSCPWYVZEJ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NDYIQSCPWYVZEJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H12O5/c1-6-3-8(14)11-10(17-6)4-9(16-2)7(5-13)12(11)15/h3-4,13,15H,5H2,1-2H3
SMILES:  Cc1cc(=O)c2c(cc(c(CO)c2O)OC)o1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12084957
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0000144] Chromones

*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
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. callus n.a. PMID[10552648]
NPO28469 Tolypocladium extinguens Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. PMID[12444701]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[18214349]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18406151]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. seed n.a. PMID[21049975]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO8234 Vernonia galamensis Species Asteraceae Eukaryota n.a. seed n.a. PMID[9930408]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9455 Uncaria orientalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8620 Caesalpinia major Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9455 Uncaria orientalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5832 Acacia nelsonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8771 Heterodermia dissecta Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27730 Silene viscidula Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7188 Zieria granulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9455 Uncaria orientalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16583 Asarum takaoi Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4321 Siphula ceratites Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27585 Ocellularia praestans Species Graphidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6033 Anthriscus neglecta Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8234 Vernonia galamensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5540 Amorpha canescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8620 Caesalpinia major Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4875 Ugni molinae Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7017 Monas vulgaris Species Chromulinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24536 Senecio cylindricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28190 Virola guggenheimii Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27531 Aethusa cynapium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5954 Petroselinum crispum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4072 Anacyclus radiatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9072 Bolocera tuediae Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27378 Scirpus kysoor Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8009 Arctotis venusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9330 Odinia antillensis Species Odiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28469 Tolypocladium extinguens Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2389 Pinus japonica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6292 Teucrium brevifolium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3668 Kalanchoe delagoensis Species Crassulaceae 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 NPC276384 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 NPC276384 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