Structure

Physi-Chem Properties

Molecular Weight:  266.15
Volume:  278.135
LogP:  0.954
LogD:  0.907
LogS:  -1.364
# Rotatable Bonds:  3
TPSA:  77.76
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.665
Synthetic Accessibility Score:  4.438
Fsp3:  0.667
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:  -4.587
MDCK Permeability:  1.0198355084867217e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.096
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.568
Plasma Protein Binding (PPB):  51.82649230957031%
Volume Distribution (VD):  0.559
Pgp-substrate:  50.11444091796875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.108
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.792
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.122
CYP3A4-inhibitor:  0.029
CYP3A4-substrate:  0.248

ADMET: Excretion

Clearance (CL):  4.343
Half-life (T1/2):  0.74

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.552
Drug-inuced Liver Injury (DILI):  0.039
AMES Toxicity:  0.549
Rat Oral Acute Toxicity:  0.217
Maximum Recommended Daily Dose:  0.163
Skin Sensitization:  0.104
Carcinogencity:  0.793
Eye Corrosion:  0.004
Eye Irritation:  0.048
Respiratory Toxicity:  0.945

Download Data

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

  Natural Product: NPC273367

Natural Product ID:  NPC273367
Common Name*:   PXBZMGHIEDYLOI-JSGCOSHPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PXBZMGHIEDYLOI-JSGCOSHPSA-N
Standard InCHI:  InChI=1S/C15H22O4/c1-10-4-3-5-14(2)12(10)6-11(7-13(14)18)15(19,8-16)9-17/h7,12,16-17,19H,1,3-6,8-9H2,2H3/t12-,14-/m0/s1
SMILES:  C=C1CCC[C@@]2(C)[C@H]1CC(=CC2=O)C(CO)(CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   639678
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
NPO12713 Brachylaena ramiflora Species Asteraceae Eukaryota twigs Madagascar rainforest n.a. PMID[12193040]
NPO13045 Kielmeyera albopunctata Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[12762797]
NPO12713 Brachylaena ramiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26016 Spheciospongia vagabunda Species Spirastrellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6858 Achillea tuzsonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25196 Nuxia oppositifolia Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10799 Espeletia moritziana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11869 Vernonia leopoldi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13045 Kielmeyera albopunctata Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3935 Asplenium septentrionale Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5136 Colliguaja salicifolia Species Euphorbiaceae 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 NPC273367 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 NPC273367 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