Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  245.61
LogP:  5.332
LogD:  4.246
LogS:  -4.984
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.542
Synthetic Accessibility Score:  4.011
Fsp3:  0.733
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:  -4.511
MDCK Permeability:  1.653144499869086e-05
Pgp-inhibitor:  0.813
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.86
30% Bioavailability (F30%):  0.048

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.203
Plasma Protein Binding (PPB):  92.64493560791016%
Volume Distribution (VD):  3.272
Pgp-substrate:  4.95703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.725
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.298
CYP2C19-substrate:  0.918
CYP2C9-inhibitor:  0.238
CYP2C9-substrate:  0.627
CYP2D6-inhibitor:  0.232
CYP2D6-substrate:  0.802
CYP3A4-inhibitor:  0.833
CYP3A4-substrate:  0.335

ADMET: Excretion

Clearance (CL):  8.375
Half-life (T1/2):  0.104

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.374
Drug-inuced Liver Injury (DILI):  0.272
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.915
Skin Sensitization:  0.533
Carcinogencity:  0.865
Eye Corrosion:  0.937
Eye Irritation:  0.969
Respiratory Toxicity:  0.717

Download Data

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

  Natural Product: NPC108405

Natural Product ID:  NPC108405
Common Name*:   QEBNYNLSCGVZOH-GUTXKFCHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QEBNYNLSCGVZOH-GUTXKFCHSA-N
Standard InCHI:  InChI=1S/C15H24/c1-11(2)13-8-9-14-7-5-6-12(3)15(14,4)10-13/h7,12-13H,1,5-6,8-10H2,2-4H3/t12-,13+,15-/m0/s1
SMILES:  C=C(C)[C@@H]1CCC2=CCC[C@H](C)[C@]2(C)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   52319950
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
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[12662092]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. PMID[15679308]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. Caribbean n.a. PMID[1686898]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. stem n.a. PMID[21226514]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[26281591]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[3404159]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota Pt n.a. n.a. Database[FooDB]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8433 Bongardia chrysogonum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO117 Acacia armata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17179 Elizabethkingia meningoseptica Species Flavobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8132 Fritillaria meleagris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1541 Clusia ellipticifolia Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2008 Streptomyces ehimensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13682 Lonchocarpus laxiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4836 Sideritis arborescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1706 Eragrostis curvula Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO643 Astragalus ernestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8950 Stilpnopappus pickelii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21493 Bunodosoma caissarum Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1049 Tethya amamensis Species Tethyidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7793 Matricaria matricarioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3445 Dumoria heckeli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19991 Mantella aurantiaca Species Mantellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2323 Plantago lundborgii Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5339 Isophysis tasmanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1203 Solanum pseudoquina Species Solanaceae 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 NPC108405 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 NPC108405 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