Structure

Physi-Chem Properties

Molecular Weight:  289.17
Volume:  303.74
LogP:  1.877
LogD:  1.315
LogS:  -2.033
# Rotatable Bonds:  5
TPSA:  49.77
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.861
Synthetic Accessibility Score:  3.937
Fsp3:  0.588
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:  -4.885
MDCK Permeability:  5.025160498917103e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.061
Human Intestinal Absorption (HIA):  0.036
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.263
Plasma Protein Binding (PPB):  29.683795928955078%
Volume Distribution (VD):  2.461
Pgp-substrate:  76.24514770507812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.084
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.873
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.137
CYP2D6-inhibitor:  0.834
CYP2D6-substrate:  0.766
CYP3A4-inhibitor:  0.046
CYP3A4-substrate:  0.775

ADMET: Excretion

Clearance (CL):  10.3
Half-life (T1/2):  0.215

ADMET: Toxicity

hERG Blockers:  0.61
Human Hepatotoxicity (H-HT):  0.467
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.05
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.331
Carcinogencity:  0.086
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.74

Download Data

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

  Natural Product: NPC46780

Natural Product ID:  NPC46780
Common Name*:   RKUNBYITZUJHSG-AUSYRVNMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RKUNBYITZUJHSG-AUSYRVNMSA-N
Standard InCHI:  InChI=1S/C17H23NO3/c1-18-13-7-8-14(18)10-15(9-13)21-17(20)16(11-19)12-5-3-2-4-6-12/h2-6,13-16,19H,7-11H2,1H3/t13?,14?,15?,16-/m0/s1
SMILES:  CN1C2CCC1CC(C2)OC(=O)[C@@H](CO)c1ccccc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25817
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0000492] Tropane alkaloids

*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
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota seeds n.a. n.a. PMID[11858758]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[12467621]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15374592]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. root n.a. PMID[16212233]
NPO24850 Datura metel Species Solanaceae Eukaryota flowers Yuxi Town, Fuqing City, Fujian Province, China 2005-SEP PMID[17583953]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17823 Lycium chinense Species Solanaceae Eukaryota root bark n.a. n.a. PMID[23282106]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[24417583]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. n.a. PMID[26923696]
NPO17823 Lycium chinense Species Solanaceae Eukaryota Root Bark n.a. n.a. PMID[26982999]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[31397570]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[9090870]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16326 Scopolia parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16326 Scopolia parviflora Species Solanaceae 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 NPC46780 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 NPC46780 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