Structure

Physi-Chem Properties

Molecular Weight:  221.1
Volume:  225.817
LogP:  -2.274
LogD:  1.177
LogS:  0.08
# Rotatable Bonds:  2
TPSA:  44.59
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.698
Synthetic Accessibility Score:  3.839
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.603
MDCK Permeability:  2.4042521545197815e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.475
20% Bioavailability (F20%):  0.95
30% Bioavailability (F30%):  0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.992
Plasma Protein Binding (PPB):  48.659706115722656%
Volume Distribution (VD):  2.031
Pgp-substrate:  43.602596282958984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.697
CYP1A2-substrate:  0.423
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.418
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.674
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.619
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.09

ADMET: Excretion

Clearance (CL):  5.75
Half-life (T1/2):  0.847

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.918
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.41
Rat Oral Acute Toxicity:  0.283
Maximum Recommended Daily Dose:  0.3
Skin Sensitization:  0.946
Carcinogencity:  0.201
Eye Corrosion:  0.66
Eye Irritation:  0.899
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC312419

Natural Product ID:  NPC312419
Common Name*:   Phenolbetain
IUPAC Name:   7,8-dimethoxy-2-methyl-3,4-dihydroisoquinolin-2-ium-6-ol
Synonyms:   Phenolbetain
Standard InCHIKey:  FBTVHOVKCOJXHO-UHFFFAOYSA-O
Standard InCHI:  InChI=1S/C12H15NO3/c1-13-5-4-8-6-10(14)12(16-3)11(15-2)9(8)7-13/h6-7H,4-5H2,1-3H3/p+1
SMILES:  C[NH+]1CCC2=CC(=O)C(=C(C2=C1)OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL238413
PubChem CID:   44433884
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002958] Dihydroisoquinolines

*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
NPO20751 Hypserpa nitida Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[17723297]
NPO20751 Hypserpa nitida 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. CC50 = 2181000.0 nM PMID[541947]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 2367000.0 nM PMID[541947]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 > 4525000.0 nM PMID[541947]
NPT2 Others Unspecified Ratio CC50/IC50 < 1.0 n.a. PMID[541947]

☑ 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 NPC312419 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
0.6559 Remote Similarity NPC296589
0.6383 Remote Similarity NPC2640
0.6146 Remote Similarity NPC472161
0.6042 Remote Similarity NPC475614
0.6042 Remote Similarity NPC185928
0.6026 Remote Similarity NPC317796
0.602 Remote Similarity NPC116231
0.6019 Remote Similarity NPC472162
0.5949 Remote Similarity NPC25038
0.5904 Remote Similarity NPC68044
0.5897 Remote Similarity NPC474805
0.5882 Remote Similarity NPC112312
0.5833 Remote Similarity NPC9436
0.5823 Remote Similarity NPC129710
0.5816 Remote Similarity NPC476141
0.5814 Remote Similarity NPC469446
0.5802 Remote Similarity NPC200831
0.5802 Remote Similarity NPC299369
0.5802 Remote Similarity NPC224103
0.5714 Remote Similarity NPC220191
0.5703 Remote Similarity NPC274441
0.5659 Remote Similarity NPC209195
0.5659 Remote Similarity NPC13826
0.5657 Remote Similarity NPC469860
0.5657 Remote Similarity NPC130436
0.5657 Remote Similarity NPC469861
0.5641 Remote Similarity NPC22329
0.5632 Remote Similarity NPC78625
0.5619 Remote Similarity NPC474129

  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 NPC312419 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
0.6854 Remote Similarity NPD5115 Clinical (unspecified phase)
0.5802 Remote Similarity NPD8779 Phase 3

  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