Structure

Physi-Chem Properties

Molecular Weight:  154.14
Volume:  179.114
LogP:  2.289
LogD:  2.044
LogS:  -2.033
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.575
Synthetic Accessibility Score:  2.929
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.386
MDCK Permeability:  1.9458835595287383e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.035
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.98
Plasma Protein Binding (PPB):  46.070556640625%
Volume Distribution (VD):  1.047
Pgp-substrate:  56.18000030517578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.068
CYP1A2-substrate:  0.824
CYP2C19-inhibitor:  0.058
CYP2C19-substrate:  0.834
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.835
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.827
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.245

ADMET: Excretion

Clearance (CL):  10.579
Half-life (T1/2):  0.391

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.187
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.042
Skin Sensitization:  0.275
Carcinogencity:  0.446
Eye Corrosion:  0.943
Eye Irritation:  0.986
Respiratory Toxicity:  0.232

Download Data

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

  Natural Product: NPC57605

Natural Product ID:  NPC57605
Common Name*:   RUJPNZNXGCHGID-MGCOHNPYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RUJPNZNXGCHGID-MGCOHNPYSA-N
Standard InCHI:  InChI=1S/C10H18O/c1-8(2)9-4-6-10(3,11)7-5-9/h9,11H,1,4-7H2,2-3H3/t9-,10-
SMILES:  C=C(C)[C@H]1CC[C@@](C)(CC1)O
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:0001401] Menthane 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
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[10096857]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23507152]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[26020634]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[8229021]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO42012 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26138 Rosmarinus officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae 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
NPO6098 NPC57605 Other Leaf Essent. Oil 3.3 1 5.6 mg/100g Database [DUKE]
NPO42012 NPC57605 Other Plant 5.75 2 9.5 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 NPC57605 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 NPC57605 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