Structure

Physi-Chem Properties

Molecular Weight:  286.16
Volume:  325.163
LogP:  2.096
LogD:  -0.166
LogS:  -2.038
# Rotatable Bonds:  7
TPSA:  54.37
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.577
Synthetic Accessibility Score:  4.273
Fsp3:  0.444
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.861
MDCK Permeability:  4.8155012336792424e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  100.37444305419922%
Volume Distribution (VD):  0.778
Pgp-substrate:  1.9401991367340088%

ADMET: Metabolism

CYP1A2-inhibitor:  0.488
CYP1A2-substrate:  0.898
CYP2C19-inhibitor:  0.954
CYP2C19-substrate:  0.811
CYP2C9-inhibitor:  0.953
CYP2C9-substrate:  0.991
CYP2D6-inhibitor:  0.603
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.907
CYP3A4-substrate:  0.534

ADMET: Excretion

Clearance (CL):  5.358
Half-life (T1/2):  0.888

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.982
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.736
Rat Oral Acute Toxicity:  0.903
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.848
Carcinogencity:  0.614
Eye Corrosion:  0.933
Eye Irritation:  0.595
Respiratory Toxicity:  0.899

Download Data

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

  Natural Product: NPC84094

Natural Product ID:  NPC84094
Common Name*:   OYHPWFRLKZQWNW-VSBPXGATSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OYHPWFRLKZQWNW-VSBPXGATSA-N
Standard InCHI:  InChI=1S/C18H22O3/c1-4-5-6-7-8-9-10-11-12-13-17(20)16(14-19)18(21)15(2)3/h4-5,10-11,15-16,19H,12-14H2,1-3H3/b5-4+,11-10+/t16-/m1/s1
SMILES:  C/C=C/C#CC#C/C=C/CCC(=O)[C@@H](CO)C(=O)C(C)C
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:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18002 Ipomoea obscura Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24028 Cissus adnata Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16697 Solanum linearifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24028 Cissus adnata Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13033 Helichrysum setosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18002 Ipomoea obscura Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16459 Lasthenia glabrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14585 Iris xiphium Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18586 Tamarix ramosissima Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2255 Saturnia pavonia Species Saturniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16332 Liparis kumokiri Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15759 Boehmeria japonica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13994 Piscidia mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6553 Pseudomonas savastanoi Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22565 Bidens graveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5058 Synoicum macroglossum Species Polyclinidae 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 NPC84094 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 NPC84094 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