Structure

Physi-Chem Properties

Molecular Weight:  166.14
Volume:  187.853
LogP:  3.17
LogD:  3.276
LogS:  -3.735
# Rotatable Bonds:  2
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.573
Synthetic Accessibility Score:  4.297
Fsp3:  0.818
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.256
MDCK Permeability:  1.9834618797176518e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.651
30% Bioavailability (F30%):  0.44

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  53.789390563964844%
Volume Distribution (VD):  1.167
Pgp-substrate:  39.74713897705078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.126
CYP1A2-substrate:  0.345
CYP2C19-inhibitor:  0.078
CYP2C19-substrate:  0.814
CYP2C9-inhibitor:  0.146
CYP2C9-substrate:  0.178
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.606
CYP3A4-inhibitor:  0.028
CYP3A4-substrate:  0.224

ADMET: Excretion

Clearance (CL):  8.211
Half-life (T1/2):  0.122

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.064
Drug-inuced Liver Injury (DILI):  0.087
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.867
Skin Sensitization:  0.126
Carcinogencity:  0.772
Eye Corrosion:  0.831
Eye Irritation:  0.982
Respiratory Toxicity:  0.959

Download Data

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

  Natural Product: NPC490323

Natural Product ID:  NPC490323
Common Name*:   Myrtenyl methyl ether
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GMYAZJHVKQKHSD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H18O/c1-11(2)9-5-4-8(7-12-3)10(11)6-9/h4,9-10H,5-7H2,1-3H3
SMILES:  COCC1=CCC2CC1C2(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:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001564] Bicyclic monoterpenoids

*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
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8545 Hyssopus officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26637 Mentha aquatica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8545 Hyssopus officinalis Species Lamiaceae 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
NPO8545 NPC490323 Other Flower 6.6 1.2 12 mg/100g Database [DUKE]
NPO8545 NPC490323 Other Leaf 19.05 0.1 38 mg/100g Database [DUKE]
NPO26637 NPC490323 Raw Shoot 0.105 0.01 0.2 mg/100g Database [DUKE]

☑ 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 NPC490323 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 NPC490323 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