Structure

Physi-Chem Properties

Molecular Weight:  242.17
Volume:  292.923
LogP:  4.764
LogD:  4.173
LogS:  -5.145
# Rotatable Bonds:  8
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.391
Synthetic Accessibility Score:  4.016
Fsp3:  0.412
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:  -4.362
MDCK Permeability:  4.125776467844844e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.954
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  101.64080047607422%
Volume Distribution (VD):  1.195
Pgp-substrate:  1.0352742671966553%

ADMET: Metabolism

CYP1A2-inhibitor:  0.927
CYP1A2-substrate:  0.313
CYP2C19-inhibitor:  0.919
CYP2C19-substrate:  0.352
CYP2C9-inhibitor:  0.915
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.48
CYP2D6-substrate:  0.821
CYP3A4-inhibitor:  0.921
CYP3A4-substrate:  0.137

ADMET: Excretion

Clearance (CL):  4.426
Half-life (T1/2):  0.39

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.102
Drug-inuced Liver Injury (DILI):  0.626
AMES Toxicity:  0.324
Rat Oral Acute Toxicity:  0.942
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.965
Carcinogencity:  0.664
Eye Corrosion:  0.989
Eye Irritation:  0.98
Respiratory Toxicity:  0.986

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

  Natural Product: NPC296680

Natural Product ID:  NPC296680
Common Name*:   JRLHSTVTOOELAF-DVQDXYAYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JRLHSTVTOOELAF-DVQDXYAYSA-N
Standard InCHI:  InChI=1S/C17H22O/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17(18)4-2/h3-4,10-11,17-18H,1-2,5-9,12H2/b11-10+/t17-/m0/s1
SMILES:  C=CCCCCC/C=C/CC#CC#C[C@H](C=C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101711904
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
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota aerial parts n.a. n.a. PMID[23819871]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[31181918]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[3430163]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18448 Hamelia patens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18274 Centaurea deusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18065 Siparuna gilgiana Species Siparunaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13870 Podocarpium podocarpum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12902 Alstonia undulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17649 Eugenia caryophyllus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17123 Delphinium roylei Species Ranunculaceae 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 NPC296680 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 NPC296680 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