Structure

Physi-Chem Properties

Molecular Weight:  149.08
Volume:  164.905
LogP:  1.105
LogD:  0.605
LogS:  -1.1
# Rotatable Bonds:  2
TPSA:  43.09
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.642
Synthetic Accessibility Score:  2.083
Fsp3:  0.222
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.908
MDCK Permeability:  6.727255822625011e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.059
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  43.41297912597656%
Volume Distribution (VD):  2.914
Pgp-substrate:  69.34754180908203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.736
CYP1A2-substrate:  0.103
CYP2C19-inhibitor:  0.061
CYP2C19-substrate:  0.35
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.424
CYP2D6-substrate:  0.557
CYP3A4-inhibitor:  0.079
CYP3A4-substrate:  0.228

ADMET: Excretion

Clearance (CL):  6.665
Half-life (T1/2):  0.753

ADMET: Toxicity

hERG Blockers:  0.096
Human Hepatotoxicity (H-HT):  0.139
Drug-inuced Liver Injury (DILI):  0.093
AMES Toxicity:  0.047
Rat Oral Acute Toxicity:  0.832
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.154
Carcinogencity:  0.075
Eye Corrosion:  0.012
Eye Irritation:  0.058
Respiratory Toxicity:  0.494

Download Data

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

  Natural Product: NPC95039

Natural Product ID:  NPC95039
Common Name*:   PUAQLLVFLMYYJJ-SSDOTTSWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PUAQLLVFLMYYJJ-SSDOTTSWSA-N
Standard InCHI:  InChI=1S/C9H11NO/c1-7(10)9(11)8-5-3-2-4-6-8/h2-7H,10H2,1H3/t7-/m1/s1
SMILES:  C[C@H](C(=O)c1ccccc1)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   149798
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO1850 Veronica longifolia Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[20806928]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[21465337]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO1676 Mikania cordata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5570 0tholirion hyacinthinum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5092 Maytenus krukovii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5092 Maytenus krukovii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5570 0tholirion hyacinthinum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1676 Mikania cordata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5570 0tholirion hyacinthinum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO411 Tilia americana Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5092 Maytenus krukovii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1229 Piper lenticellosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1676 Mikania cordata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8997 Omphalotus japonicus Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5570 0tholirion hyacinthinum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4400 Dicksonia scabra Species Dicksoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1850 Veronica longifolia Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8185 Euphorbia serrula Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1080 Piper permucronatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3094 Siparuna nicaraguensis Species Siparunaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2390 Dorstenia gigas Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae 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
NPT29 Organism Rattus norvegicus Rattus norvegicus ED50 = 0.72 mg.kg-1 PMID[564242]
NPT29 Organism Rattus norvegicus Rattus norvegicus ED50 = 4.41 mg.kg-1 PMID[564242]

☑ 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 NPC95039 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 NPC95039 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