Structure

Physi-Chem Properties

Molecular Weight:  271.16
Volume:  292.314
LogP:  3.01
LogD:  2.131
LogS:  -3.385
# Rotatable Bonds:  4
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.625
Synthetic Accessibility Score:  4.032
Fsp3:  0.471
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.786
MDCK Permeability:  1.93270570889581e-05
Pgp-inhibitor:  0.588
Pgp-substrate:  0.372
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.886
Plasma Protein Binding (PPB):  59.68400573730469%
Volume Distribution (VD):  5.716
Pgp-substrate:  30.984872817993164%

ADMET: Metabolism

CYP1A2-inhibitor:  0.171
CYP1A2-substrate:  0.113
CYP2C19-inhibitor:  0.065
CYP2C19-substrate:  0.793
CYP2C9-inhibitor:  0.076
CYP2C9-substrate:  0.1
CYP2D6-inhibitor:  0.967
CYP2D6-substrate:  0.788
CYP3A4-inhibitor:  0.243
CYP3A4-substrate:  0.553

ADMET: Excretion

Clearance (CL):  8.565
Half-life (T1/2):  0.132

ADMET: Toxicity

hERG Blockers:  0.712
Human Hepatotoxicity (H-HT):  0.969
Drug-inuced Liver Injury (DILI):  0.893
AMES Toxicity:  0.158
Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.991
Skin Sensitization:  0.938
Carcinogencity:  0.487
Eye Corrosion:  0.008
Eye Irritation:  0.047
Respiratory Toxicity:  0.918

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

  Natural Product: NPC158735

Natural Product ID:  NPC158735
Common Name*:   WPUIZWXOSDVQJU-MUJYYYPQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WPUIZWXOSDVQJU-MUJYYYPQSA-N
Standard InCHI:  InChI=1S/C17H21NO2/c1-12(13-6-4-3-5-7-13)17(19)20-16-10-14-8-9-15(11-16)18(14)2/h3-7,14-16H,1,8-11H2,2H3/t14-,15+,16-
SMILES:  C=C(c1ccccc1)C(=O)O[C@H]1C[C@@H]2CC[C@H](C1)N2C
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
NPO23470 Orthosiphon labiatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17256988]
NPO13054 Rhamnus davurica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26212 Fagopyrum tataricum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26212 Fagopyrum tataricum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13054 Rhamnus davurica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26516 Homalium cochinchinense Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13054 Rhamnus davurica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26516 Homalium cochinchinense Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13054 Rhamnus davurica Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8365 Gymnadenia albida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26407 Deguelia rufescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26452 Dermophis mexicanus Species Dermophiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25950 Pinus apacheca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14522 Uvaria cuneifolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28346 Phacelia minor Species Hydrophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23470 Orthosiphon labiatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26320 Acer palmatum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26107 Montanoa speciosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26212 Fagopyrum tataricum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25770 Dioncophyllum thollonii Species Dioncophyllaceae 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 NPC158735 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 NPC158735 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