Structure

Physi-Chem Properties

Molecular Weight:  255.15
Volume:  257.176
LogP:  0.376
LogD:  0.598
LogS:  -0.398
# Rotatable Bonds:  3
TPSA:  70.0
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.539
Synthetic Accessibility Score:  4.938
Fsp3:  0.769
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:  -4.831
MDCK Permeability:  6.845878669992089e-05
Pgp-inhibitor:  0.109
Pgp-substrate:  0.202
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.622

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.273
Plasma Protein Binding (PPB):  24.600244522094727%
Volume Distribution (VD):  1.113
Pgp-substrate:  64.43477630615234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.05
CYP1A2-substrate:  0.098
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.683
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.273
CYP2D6-inhibitor:  0.283
CYP2D6-substrate:  0.37
CYP3A4-inhibitor:  0.038
CYP3A4-substrate:  0.308

ADMET: Excretion

Clearance (CL):  8.044
Half-life (T1/2):  0.854

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.699
Drug-inuced Liver Injury (DILI):  0.588
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.936
Skin Sensitization:  0.874
Carcinogencity:  0.326
Eye Corrosion:  0.12
Eye Irritation:  0.417
Respiratory Toxicity:  0.932

Download Data

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

  Natural Product: NPC224567

Natural Product ID:  NPC224567
Common Name*:   YZFJTFVPCWEPND-BDYNUDSHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YZFJTFVPCWEPND-BDYNUDSHSA-N
Standard InCHI:  InChI=1S/C13H21NO4/c1-4-7(2)13(17)18-8-5-9-11(15)12(16)10(6-8)14(9)3/h4,8-12,15-16H,5-6H2,1-3H3/b7-4+/t8-,9-,10+,11-,12+
SMILES:  C/C=C(C)/C(=O)O[C@H]1C[C@H]2[C@@H]([C@@H]([C@@H](C1)N2C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
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
NPO21393 Datura inoxia Species Solanaceae Eukaryota n.a. flower n.a. PMID[21280589]
NPO21393 Datura inoxia Species Solanaceae Eukaryota n.a. leaf n.a. PMID[21280589]
NPO11089 Sanicula europaea Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[9392884]
NPO21393 Datura inoxia Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13850 Bazzania trilobata Species Lepidoziaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11703 Terpios hoshinota Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11089 Sanicula europaea Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21393 Datura inoxia Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13850 Bazzania trilobata Species Lepidoziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8689 Datura suaveolens 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 NPC224567 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 NPC224567 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