Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  269.578
LogP:  1.078
LogD:  1.153
LogS:  -3.134
# Rotatable Bonds:  0
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.673
Synthetic Accessibility Score:  4.624
Fsp3:  0.733
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:  -4.79
MDCK Permeability:  3.184482557117008e-05
Pgp-inhibitor:  0.861
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.16
30% Bioavailability (F30%):  0.073

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.852
Plasma Protein Binding (PPB):  58.692283630371094%
Volume Distribution (VD):  0.878
Pgp-substrate:  41.883583068847656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.547
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.796
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.079
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.074
CYP3A4-inhibitor:  0.488
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  5.369
Half-life (T1/2):  0.657

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.501
Drug-inuced Liver Injury (DILI):  0.171
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.915
Maximum Recommended Daily Dose:  0.324
Skin Sensitization:  0.832
Carcinogencity:  0.526
Eye Corrosion:  0.033
Eye Irritation:  0.153
Respiratory Toxicity:  0.845

Download Data

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

  Natural Product: NPC209309

Natural Product ID:  NPC209309
Common Name*:   NGPDZEACIWDCKX-JRNUYWEUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NGPDZEACIWDCKX-JRNUYWEUSA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-8-9-4-6-14(2)10(16)5-7-15(3,18)12(14)11(9)19-13(8)17/h5,7-9,11-12,18H,4,6H2,1-3H3/t8-,9-,11-,12-,14-,15+/m0/s1
SMILES:  C[C@H]1[C@@H]2CC[C@@]3(C)C(=O)C=C[C@](C)([C@H]3[C@H]2OC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12443236
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001772] Eudesmanolides, secoeudesmanolides, and derivatives

*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
NPO15918 Nidema boothii Species Orchidaceae Eukaryota whole plant n.a. n.a. PMID[14987052]
NPO7892 Paubrasilia echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13069 Piper wrightii Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7892 Paubrasilia echinata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15918 Nidema boothii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2137 Helipterum corymbiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13249 Crudia amazonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14226 Cotyledon orbiculata Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14097 Verrucosispora gifhornensis Species Micromonosporaceae Bacteria 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 NPC209309 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 NPC209309 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