Structure

Physi-Chem Properties

Molecular Weight:  334.18
Volume:  350.836
LogP:  2.211
LogD:  1.89
LogS:  -2.803
# Rotatable Bonds:  6
TPSA:  69.67
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.584
Synthetic Accessibility Score:  4.98
Fsp3:  0.632
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.703
MDCK Permeability:  3.1704927096143365e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.045
20% Bioavailability (F20%):  0.802
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.946
Plasma Protein Binding (PPB):  56.81131362915039%
Volume Distribution (VD):  0.642
Pgp-substrate:  56.2763557434082%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.083
CYP2C19-inhibitor:  0.113
CYP2C19-substrate:  0.273
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.13
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.198
CYP3A4-inhibitor:  0.589
CYP3A4-substrate:  0.314

ADMET: Excretion

Clearance (CL):  2.911
Half-life (T1/2):  0.9

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.443
Drug-inuced Liver Injury (DILI):  0.787
AMES Toxicity:  0.07
Rat Oral Acute Toxicity:  0.251
Maximum Recommended Daily Dose:  0.072
Skin Sensitization:  0.175
Carcinogencity:  0.468
Eye Corrosion:  0.075
Eye Irritation:  0.228
Respiratory Toxicity:  0.116

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

  Natural Product: NPC159669

Natural Product ID:  NPC159669
Common Name*:   RYXSCMSHMBXDLZ-URNZOZBJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RYXSCMSHMBXDLZ-URNZOZBJSA-N
Standard InCHI:  InChI=1S/C19H26O5/c1-12-6-5-7-15(10-23-13(2)20)18(22)8-17-16(12)9-19(17,4)11-24-14(3)21/h7,16-17H,1,5-6,8-11H2,2-4H3/b15-7+/t16-,17+,19-/m0/s1
SMILES:  C=C1CC/C=C(COC(=O)C)/C(=O)C[C@@H]2[C@H]1C[C@@]2(C)COC(=O)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 n.a. n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota Leaves 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]
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]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16719 Alluaudia dumosa Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11989 Erythrostemon gilliesii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16558 Mallotus stenanthus Species Salangidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24279 Streptomyces inusitatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5049 Garcinia multiflora Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3903 Hemizonia congesta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14937 Gelonium aequoreum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13635 Rhodiola quadrifida Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16231 Helichrysum acutatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13988 Westiella intricata Species Hapalosiphonaceae Bacteria 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]
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]

☑ 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 NPC159669 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 NPC159669 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