Structure

Physi-Chem Properties

Molecular Weight:  564.14
Volume:  570.834
LogP:  5.409
LogD:  3.444
LogS:  -3.126
# Rotatable Bonds:  9
TPSA:  153.75
# H-Bond Aceptor:  9
# H-Bond Donor:  5
# Rings:  5
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.092
Synthetic Accessibility Score:  2.667
Fsp3:  0.03
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.269
MDCK Permeability:  1.4696855032525491e-05
Pgp-inhibitor:  0.09
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.792
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  103.07454681396484%
Volume Distribution (VD):  0.258
Pgp-substrate:  0.5506063103675842%

ADMET: Metabolism

CYP1A2-inhibitor:  0.778
CYP1A2-substrate:  0.02
CYP2C19-inhibitor:  0.96
CYP2C19-substrate:  0.04
CYP2C9-inhibitor:  0.688
CYP2C9-substrate:  0.963
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.368
CYP3A4-inhibitor:  0.136
CYP3A4-substrate:  0.183

ADMET: Excretion

Clearance (CL):  5.84
Half-life (T1/2):  0.904

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.028
Drug-inuced Liver Injury (DILI):  0.97
AMES Toxicity:  0.117
Rat Oral Acute Toxicity:  0.469
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.723
Carcinogencity:  0.264
Eye Corrosion:  0.003
Eye Irritation:  0.888
Respiratory Toxicity:  0.024

Download Data

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

  Natural Product: NPC298978

Natural Product ID:  NPC298978
Common Name*:   AJETYWZVYZWNNH-OBOLIWSASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AJETYWZVYZWNNH-OBOLIWSASA-N
Standard InCHI:  InChI=1S/C12H14O2S/c1-4-5-6-8-11(15-3)9-7-10-12(13)14-2/h4-5,7,9-10H,1-3H3/b5-4-,10-7-,11-9+
SMILES:  C/C=CC#C/C(=CC=C/C(=O)OC)/SC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

*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
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[11000050]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[11374973]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. Einan Reservoir in Israel n.a. PMID[12141855]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[12141855]
NPO14305 Moricandia arvensis Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15844940]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[18163584]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[18558743]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[18973386]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria water bloom of the cyanobacterium Microcystis aeruginosa n.a. n.a. PMID[19650639]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria bloom material Lake Kinneret, Israel n.a. PMID[22280481]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. Kibbutz Geva, Israel n.a. PMID[23153007]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. Water Reservoir near Kibbutz Hafetz Haim, Israel n.a. PMID[23718637]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria Bloom n.a. n.a. PMID[24261937]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[24642434]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[24868986]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[29405714]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria Bloom n.a. n.a. PMID[29847132]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[9249979]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. PMID[9842728]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. pericarp n.a. PMID[p25172756]
NPO6202 Aglaomorpha coronans Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. Database[Title]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15632 Podopetalum ormondi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25641 Peltophorum vogelianum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9371 Pilocarpus organensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6202 Aglaomorpha coronans Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2493 Parmelia reptans Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12129 Fagara mantchurica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12360 Pithecellobium jiringa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14305 Moricandia arvensis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17138 Lethasterias nanimensis Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9790 Anthemis austriaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8425 Gymnosporia rothiana Species Celastraceae 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 NPC298978 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 NPC298978 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