Structure

Physi-Chem Properties

Molecular Weight:  248.21
Volume:  294.913
LogP:  6.38
LogD:  4.527
LogS:  -5.983
# Rotatable Bonds:  11
TPSA:  12.53
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.278
Synthetic Accessibility Score:  3.663
Fsp3:  0.647
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.561
MDCK Permeability:  1.82745043275645e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.094
30% Bioavailability (F30%):  0.919

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.234
Plasma Protein Binding (PPB):  97.36454772949219%
Volume Distribution (VD):  1.39
Pgp-substrate:  2.7092490196228027%

ADMET: Metabolism

CYP1A2-inhibitor:  0.348
CYP1A2-substrate:  0.25
CYP2C19-inhibitor:  0.447
CYP2C19-substrate:  0.127
CYP2C9-inhibitor:  0.356
CYP2C9-substrate:  0.854
CYP2D6-inhibitor:  0.063
CYP2D6-substrate:  0.66
CYP3A4-inhibitor:  0.686
CYP3A4-substrate:  0.117

ADMET: Excretion

Clearance (CL):  8.986
Half-life (T1/2):  0.129

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.011
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.064
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.085
Skin Sensitization:  0.974
Carcinogencity:  0.427
Eye Corrosion:  0.972
Eye Irritation:  0.994
Respiratory Toxicity:  0.033

Download Data

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

  Natural Product: NPC184581

Natural Product ID:  NPC184581
Common Name*:   WNXISRDEAZBCKW-SJORKVTESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WNXISRDEAZBCKW-SJORKVTESA-N
Standard InCHI:  InChI=1S/C17H28O/c1-3-5-7-8-9-10-11-13-15-17-16(18-17)14-12-6-4-2/h3,6,11-13,16-17H,1,4-5,7-10,14-15H2,2H3/t16-,17+/m1/s1
SMILES:  C=CCCCCCC=CC[C@H]1[C@@H](CC=CCC)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000159] Epoxides

*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
NPO1528 Dalea elegans Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21561780]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. fruit n.a. PMID[22396124]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8685 Hymenocallis arenicola Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9064 Cirsium arvense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6024 Cratoxylum formosum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8685 Hymenocallis arenicola Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1785 Corallina rubens Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1528 Dalea elegans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4471 Blumea densiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO480 Hygrophila erecta Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24513 Streptomyces cyaneofuscatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9525 Relicina samoensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO743 Wardomyces inflatus Species Microascaceae 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 NPC184581 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 NPC184581 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