Structure

Physi-Chem Properties

Molecular Weight:  314.19
Volume:  341.995
LogP:  4.481
LogD:  4.708
LogS:  -4.931
# Rotatable Bonds:  3
TPSA:  39.44
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.435
Synthetic Accessibility Score:  4.534
Fsp3:  0.55
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:  2.1031501091783866e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.155
30% Bioavailability (F30%):  0.033

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.29
Plasma Protein Binding (PPB):  94.04029083251953%
Volume Distribution (VD):  3.197
Pgp-substrate:  6.914112567901611%

ADMET: Metabolism

CYP1A2-inhibitor:  0.563
CYP1A2-substrate:  0.814
CYP2C19-inhibitor:  0.945
CYP2C19-substrate:  0.602
CYP2C9-inhibitor:  0.923
CYP2C9-substrate:  0.353
CYP2D6-inhibitor:  0.642
CYP2D6-substrate:  0.458
CYP3A4-inhibitor:  0.93
CYP3A4-substrate:  0.559

ADMET: Excretion

Clearance (CL):  11.977
Half-life (T1/2):  0.14

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.654
Drug-inuced Liver Injury (DILI):  0.681
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.817
Maximum Recommended Daily Dose:  0.95
Skin Sensitization:  0.75
Carcinogencity:  0.854
Eye Corrosion:  0.097
Eye Irritation:  0.15
Respiratory Toxicity:  0.981

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

  Natural Product: NPC264913

Natural Product ID:  NPC264913
Common Name*:   FVZVOUFAYLGDFW-BOUXLOLZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FVZVOUFAYLGDFW-BOUXLOLZSA-N
Standard InCHI:  InChI=1S/C20H26O3/c1-6-12(2)19(21)23-18-17-13(3)11-22-16(17)10-15-9-7-8-14(4)20(15,18)5/h6,9,11,14,18H,7-8,10H2,1-5H3/t14-,18+,20+/m0/s1
SMILES:  CC=C(C)C(=O)O[C@@H]1c2c(C)coc2CC2=CCC[C@H](C)[C@@]12C
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:0001550] Sesquiterpenoids
          • [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane sesquiterpenoids

*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
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. whole plant n.a. DOI[10.1007/BF02329610]
NPO21390 Zanthoxylum integrifoliolum Species Rutaceae Eukaryota fruit Lanyu Island, Taitung County, Taiwan n.a. PMID[10395498]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[15270561]
NPO21390 Zanthoxylum integrifoliolum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[17822293]
NPO7428 Bletilla formosana Species Orchidaceae Eukaryota Rhizomes n.a. n.a. PMID[27525452]
NPO722 Lantana trifolia Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[3204384]
NPO12100 Citrus sulcata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7428 Bletilla formosana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21390 Zanthoxylum integrifoliolum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12100 Citrus sulcata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7428 Bletilla formosana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7428 Bletilla formosana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO722 Lantana trifolia Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21390 Zanthoxylum integrifoliolum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21072 Rhododendron dauricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12100 Citrus sulcata Species Rutaceae 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 NPC264913 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 NPC264913 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