Structure

Physi-Chem Properties

Molecular Weight:  276.17
Volume:  301.3
LogP:  3.477
LogD:  2.962
LogS:  -3.482
# Rotatable Bonds:  3
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.574
Synthetic Accessibility Score:  4.79
Fsp3:  0.647
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.615
MDCK Permeability:  3.0366096325451508e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.594
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.841
Plasma Protein Binding (PPB):  66.15857696533203%
Volume Distribution (VD):  0.611
Pgp-substrate:  49.90739440917969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.047
CYP1A2-substrate:  0.107
CYP2C19-inhibitor:  0.088
CYP2C19-substrate:  0.448
CYP2C9-inhibitor:  0.116
CYP2C9-substrate:  0.292
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.551
CYP3A4-inhibitor:  0.323
CYP3A4-substrate:  0.294

ADMET: Excretion

Clearance (CL):  5.668
Half-life (T1/2):  0.748

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.147
Drug-inuced Liver Injury (DILI):  0.413
AMES Toxicity:  0.065
Rat Oral Acute Toxicity:  0.127
Maximum Recommended Daily Dose:  0.064
Skin Sensitization:  0.146
Carcinogencity:  0.392
Eye Corrosion:  0.122
Eye Irritation:  0.247
Respiratory Toxicity:  0.223

Download Data

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

  Natural Product: NPC148790

Natural Product ID:  NPC148790
Common Name*:   JDVSJWBIOCGFMX-GEJCVMBQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JDVSJWBIOCGFMX-GEJCVMBQSA-N
Standard InCHI:  InChI=1S/C17H24O3/c1-11-6-5-7-13(10-20-12(2)18)16(19)8-15-14(11)9-17(15,3)4/h7,14-15H,1,5-6,8-10H2,2-4H3/b13-7+/t14-,15+/m0/s1
SMILES:  C=C1CC/C=C(COC(=O)C)/C(=O)C[C@@H]2[C@H]1CC2(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:0001550] 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
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota stems n.a. n.a. PMID[12932126]
NPO14937 Gelonium aequoreum Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[17714747]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota aerial parts n.a. n.a. PMID[19299148]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[20681570]
NPO16026 Gnetum montanum Species Gnetaceae Eukaryota leaves Guangxi Province, China 2000-JAN PMID[22040053]
NPO16026 Gnetum montanum Species Gnetaceae Eukaryota n.a. leaf n.a. PMID[22040053]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. stem n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[2691636]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. root n.a. PMID[8945774]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota Twigs and leaves Taichung, Taiwan 1993-Aug PMID[9322359]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5195.1 Odontites vernus subsp. serotinus Subspecies Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9482 Durio kutejensis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15464 Argylia radiata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16026 Gnetum montanum Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO845 Cyrtanthus obliquus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5874 Fumago vagans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10679 Scutellaria nepetoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14473 Stellaria delavayi Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16719 Alluaudia dumosa Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16558 Mallotus stenanthus Species Salangidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11989 Erythrostemon gilliesii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24279 Streptomyces inusitatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14937 Gelonium aequoreum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3903 Hemizonia congesta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13988 Westiella intricata Species Hapalosiphonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16231 Helichrysum acutatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5195.1 Odontites vernus subsp. serotinus Subspecies Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14140 Vernonia arbor Species Asteraceae 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 NPC148790 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 NPC148790 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