Structure

Physi-Chem Properties

Molecular Weight:  342.17
Volume:  351.907
LogP:  -0.227
LogD:  1.836
LogS:  -0.897
# Rotatable Bonds:  2
TPSA:  58.92
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.651
Synthetic Accessibility Score:  3.704
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.81
MDCK Permeability:  6.915805897733662e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.987
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.133
Plasma Protein Binding (PPB):  27.20907974243164%
Volume Distribution (VD):  1.72
Pgp-substrate:  54.30734634399414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.909
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.52
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.226
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.91
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.664

ADMET: Excretion

Clearance (CL):  13.621
Half-life (T1/2):  0.955

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.022
Drug-inuced Liver Injury (DILI):  0.014
AMES Toxicity:  0.074
Rat Oral Acute Toxicity:  0.11
Maximum Recommended Daily Dose:  0.973
Skin Sensitization:  0.921
Carcinogencity:  0.034
Eye Corrosion:  0.003
Eye Irritation:  0.029
Respiratory Toxicity:  0.055

Download Data

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

  Natural Product: NPC293305

Natural Product ID:  NPC293305
Common Name*:   BGWQPJBRBKPLEO-UHFFFAOYSA-O
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BGWQPJBRBKPLEO-UHFFFAOYSA-O
Standard InCHI:  InChI=1S/C20H23NO4/c1-21-7-6-13-9-18(24-2)19(25-3)10-14(13)16(21)8-12-4-5-17(22)20(23)15(12)11-21/h4-5,9-10,16H,6-8,11H2,1-3H3,(H-,22,23)/p+1
SMILES:  C[N+]12CCc3cc(c(cc3C2Cc2ccc(c(c2C1)O)O)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5316854
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001909] Protoberberine alkaloids and derivatives

*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
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. xylem n.a. DOI[10.1248/cpb.24.1532]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[10993146]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. Tsukuba, Japan 1998-JUN PMID[12381108]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. leaf n.a. PMID[17125224]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[22224661]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[22799262]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[23290052]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. leaf n.a. PMID[24197199]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24254087]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota stem barks n.a. n.a. PMID[25666824]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota leaves n.a. n.a. PMID[27400231]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2905 Tinospora hainanensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17873 Adonis vernalis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9661 Fraxinus szaboana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2905 Tinospora hainanensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17873 Adonis vernalis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9661 Fraxinus szaboana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17873 Adonis vernalis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9661 Fraxinus szaboana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9661 Fraxinus szaboana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17873 Adonis vernalis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15443 Ailanthus altissima Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2905 Tinospora hainanensis Species Menispermaceae 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 NPC293305 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 NPC293305 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