Structure

Physi-Chem Properties

Molecular Weight:  294.18
Volume:  324.567
LogP:  2.363
LogD:  1.885
LogS:  -2.1
# Rotatable Bonds:  9
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.424
Synthetic Accessibility Score:  4.175
Fsp3:  0.529
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.466
MDCK Permeability:  3.9315771573456004e-05
Pgp-inhibitor:  0.095
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.053
30% Bioavailability (F30%):  0.944

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.836
Plasma Protein Binding (PPB):  66.64796447753906%
Volume Distribution (VD):  0.765
Pgp-substrate:  36.63626480102539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.039
CYP1A2-substrate:  0.19
CYP2C19-inhibitor:  0.187
CYP2C19-substrate:  0.739
CYP2C9-inhibitor:  0.118
CYP2C9-substrate:  0.225
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.072
CYP3A4-inhibitor:  0.683
CYP3A4-substrate:  0.413

ADMET: Excretion

Clearance (CL):  7.445
Half-life (T1/2):  0.668

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.376
Drug-inuced Liver Injury (DILI):  0.379
AMES Toxicity:  0.216
Rat Oral Acute Toxicity:  0.816
Maximum Recommended Daily Dose:  0.912
Skin Sensitization:  0.941
Carcinogencity:  0.915
Eye Corrosion:  0.932
Eye Irritation:  0.895
Respiratory Toxicity:  0.98

Download Data

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

  Natural Product: NPC219550

Natural Product ID:  NPC219550
Common Name*:   AXXJTACQKRRZET-WCEBEWAISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AXXJTACQKRRZET-WCEBEWAISA-N
Standard InCHI:  InChI=1S/C17H26O4/c1-7-17(6,20)11-16(21-14(5)18)10-13(4)9-15(19)8-12(2)3/h7-8,10,16,20H,1,9,11H2,2-6H3/b13-10+/t16-,17-/m1/s1
SMILES:  C=C[C@](C)(C[C@@H](/C=C(C)/CC(=O)C=C(C)C)OC(=O)C)O
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:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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]
NPO11170 Akebia trifoliata Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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[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]
NPO6202 Aglaomorpha coronans Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3288 Microcystis aeruginosa Species Microcystaceae Bacteria 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]
NPO15632 Podopetalum ormondi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25641 Peltophorum vogelianum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9371 Pilocarpus organensis Species Rutaceae 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 NPC219550 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 NPC219550 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