Structure

Physi-Chem Properties

Molecular Weight:  258.09
Volume:  273.509
LogP:  3.295
LogD:  2.52
LogS:  -4.647
# Rotatable Bonds:  5
TPSA:  56.51
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.274
Synthetic Accessibility Score:  3.216
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.439
MDCK Permeability:  1.391820751450723e-05
Pgp-inhibitor:  0.75
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  95.98368072509766%
Volume Distribution (VD):  1.558
Pgp-substrate:  1.861158013343811%

ADMET: Metabolism

CYP1A2-inhibitor:  0.985
CYP1A2-substrate:  0.396
CYP2C19-inhibitor:  0.954
CYP2C19-substrate:  0.159
CYP2C9-inhibitor:  0.945
CYP2C9-substrate:  0.324
CYP2D6-inhibitor:  0.662
CYP2D6-substrate:  0.274
CYP3A4-inhibitor:  0.891
CYP3A4-substrate:  0.234

ADMET: Excretion

Clearance (CL):  7.508
Half-life (T1/2):  0.386

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.791
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.629
Rat Oral Acute Toxicity:  0.2
Maximum Recommended Daily Dose:  0.107
Skin Sensitization:  0.896
Carcinogencity:  0.809
Eye Corrosion:  0.523
Eye Irritation:  0.963
Respiratory Toxicity:  0.727

Download Data

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

  Natural Product: NPC37407

Natural Product ID:  NPC37407
Common Name*:   NQZCQIDFBYCBAU-JHGYFVHDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NQZCQIDFBYCBAU-JHGYFVHDSA-N
Standard InCHI:  InChI=1S/C15H14O4/c1-3-4-5-6-7-13(16)14-10-8-12(19-14)9-11-15(17)18-2/h4-5,8-11H,3H2,1-2H3/b5-4-,11-9+
SMILES:  CC/C=CC#CC(=O)c1ccc(/C=C/C(=O)OC)o1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   643733
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0001989] Heterocyclic fatty acids
            • [CHEMONTID:0001528] Furanoid fatty acids

*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]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. leaf n.a. PMID[16494492]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. stem n.a. PMID[16494492]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[17190445]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[17190445]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[17489633]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota leaves and stems n.a. n.a. PMID[20146529]
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]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[23265871]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22782 Lens culinaris Species Fabaceae 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 Fruit n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25239 Kadsura peltigera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22782 Lens culinaris Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25239 Kadsura peltigera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25239 Kadsura peltigera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24804 Schisandra rubriflora Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22782 Lens culinaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25239 Kadsura peltigera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24804 Schisandra rubriflora Species Schisandraceae 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 NPC37407 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 NPC37407 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