Structure

Physi-Chem Properties

Molecular Weight:  169.09
Volume:  163.733
LogP:  -1.558
LogD:  -1.555
LogS:  0.319
# Rotatable Bonds:  2
TPSA:  71.01
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.624
Synthetic Accessibility Score:  3.28
Fsp3:  0.429
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:  -6.127
MDCK Permeability:  0.0006370579940266907
Pgp-inhibitor:  0.001
Pgp-substrate:  0.719
Human Intestinal Absorption (HIA):  0.03
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.731
Plasma Protein Binding (PPB):  19.120437622070312%
Volume Distribution (VD):  0.942
Pgp-substrate:  68.64430236816406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.434
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.083
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.603
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.181
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.139

ADMET: Excretion

Clearance (CL):  2.008
Half-life (T1/2):  0.864

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.919
Drug-inuced Liver Injury (DILI):  0.45
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.197
Maximum Recommended Daily Dose:  0.1
Skin Sensitization:  0.108
Carcinogencity:  0.927
Eye Corrosion:  0.004
Eye Irritation:  0.116
Respiratory Toxicity:  0.282

Download Data

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

  Natural Product: NPC193559

Natural Product ID:  NPC193559
Common Name*:   Aminozooanemonin
IUPAC Name:   2-(2-amino-1,3-dimethylimidazol-1-ium-4-yl)acetate
Synonyms:   Aminozooanemonin
Standard InCHIKey:  UZHLDXPPXNMSFH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H11N3O2/c1-9-4-5(3-6(11)12)10(2)7(9)8/h4,8H,3H2,1-2H3,(H,11,12)
SMILES:  Cn1cc(CC(=O)O)n(C)c1=N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL442935
PubChem CID:   10080783
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0002628] Trisubstituted imidazoles
              • [CHEMONTID:0002630] 1,2,5-trisubstituted imidazoles

*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
NPO27799 Agelas dispar Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[18800848]
NPO27799 Agelas dispar Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[9461661]
NPO27799 Agelas dispar Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[9748394]
NPO27799 Agelas dispar Species Agelasidae 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
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 2.5 ug.mL-1 PMID[545807]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 8.5 ug.mL-1 PMID[545807]

☑ 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 NPC193559 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
0.5976 Remote Similarity NPC202075
0.5942 Remote Similarity NPC10915
0.5938 Remote Similarity NPC195448
0.5882 Remote Similarity NPC245768
0.5732 Remote Similarity NPC122471
0.5714 Remote Similarity NPC304455
0.5676 Remote Similarity NPC273037
0.561 Remote Similarity NPC192521

  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 NPC193559 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
0.5976 Remote Similarity NPD8962 Discontinued
0.5938 Remote Similarity NPD8621 Approved

  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