Structure

Physi-Chem Properties

Molecular Weight:  232.15
Volume:  257.918
LogP:  1.975
LogD:  2.078
LogS:  -2.558
# Rotatable Bonds:  3
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.748
Synthetic Accessibility Score:  3.632
Fsp3:  0.6
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:  -4.817
MDCK Permeability:  2.2685715521220118e-05
Pgp-inhibitor:  0.9
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.04
Plasma Protein Binding (PPB):  85.22010040283203%
Volume Distribution (VD):  1.488
Pgp-substrate:  22.41269874572754%

ADMET: Metabolism

CYP1A2-inhibitor:  0.037
CYP1A2-substrate:  0.89
CYP2C19-inhibitor:  0.377
CYP2C19-substrate:  0.939
CYP2C9-inhibitor:  0.112
CYP2C9-substrate:  0.798
CYP2D6-inhibitor:  0.099
CYP2D6-substrate:  0.54
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.574

ADMET: Excretion

Clearance (CL):  2.469
Half-life (T1/2):  0.83

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.84
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.262
Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.242
Skin Sensitization:  0.371
Carcinogencity:  0.831
Eye Corrosion:  0.079
Eye Irritation:  0.266
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC55542

Natural Product ID:  NPC55542
Common Name*:   QZJJJZCOOVXKLT-YFHOEESVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QZJJJZCOOVXKLT-YFHOEESVSA-N
Standard InCHI:  InChI=1S/C15H20O2/c1-10(15(5-6-15)11(2)16)7-12-8-13(17)14(3,4)9-12/h7-8H,5-6,9H2,1-4H3/b10-7-
SMILES:  C/C(=C/C1=CC(=O)C(C)(C)C1)/C1(CC1)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101297664
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO863 Rhaphidophora decursiva Species Araceae Eukaryota n.a. n.a. n.a. PMID[11421741]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[31577434]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2059 Lactuca denticulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO863 Rhaphidophora decursiva Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14315 Conostylis setosa Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15080 Larix kamtschatica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15211 Eriogonum brevicaule Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13317 Geigeria acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14654 Rhododendron ledebourii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15590 Peperomia tetraphylla Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5050 Galium triflorum Species Rubiaceae 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 NPC55542 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 NPC55542 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