Structure

Physi-Chem Properties

Molecular Weight:  336.19
Volume:  359.393
LogP:  3.295
LogD:  3.266
LogS:  -3.507
# Rotatable Bonds:  12
TPSA:  72.83
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.491
Synthetic Accessibility Score:  2.723
Fsp3:  0.579
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.619
MDCK Permeability:  2.9058299332973547e-05
Pgp-inhibitor:  0.198
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.899
30% Bioavailability (F30%):  0.212

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.66
Plasma Protein Binding (PPB):  88.32459259033203%
Volume Distribution (VD):  0.532
Pgp-substrate:  9.620885848999023%

ADMET: Metabolism

CYP1A2-inhibitor:  0.395
CYP1A2-substrate:  0.191
CYP2C19-inhibitor:  0.319
CYP2C19-substrate:  0.317
CYP2C9-inhibitor:  0.385
CYP2C9-substrate:  0.928
CYP2D6-inhibitor:  0.712
CYP2D6-substrate:  0.872
CYP3A4-inhibitor:  0.77
CYP3A4-substrate:  0.249

ADMET: Excretion

Clearance (CL):  8.73
Half-life (T1/2):  0.91

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.328
Drug-inuced Liver Injury (DILI):  0.383
AMES Toxicity:  0.227
Rat Oral Acute Toxicity:  0.017
Maximum Recommended Daily Dose:  0.888
Skin Sensitization:  0.323
Carcinogencity:  0.507
Eye Corrosion:  0.182
Eye Irritation:  0.719
Respiratory Toxicity:  0.539

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  Natural Product: NPC279098

Natural Product ID:  NPC279098
Common Name*:   GPHSJPVUEZFIDE-YITBWLPSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GPHSJPVUEZFIDE-YITBWLPSSA-N
Standard InCHI:  InChI=1S/C20H30O8/c1-9-6-20(28-17-15(25)14(24)13(23)11(8-21)27-17)7-10(2)19(4-5-19)18(3,26)16(20)12(9)22/h7,9,11,13-17,21,23-26H,4-6,8H2,1-3H3/t9-,11-,13-,14+,15-,16+,17+,18+,20-/m1/s1
SMILES:  C[C@@H]1C[C@]2(C=C(C)C3(CC3)[C@](C)([C@@H]2C1=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13962856
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[10978200]
NPO863 Rhaphidophora decursiva Species Araceae Eukaryota n.a. n.a. n.a. PMID[11421741]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[31577434]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10948 Guarea rhopalocarpa Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7952 Commelina communis Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7952 Commelina communis Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10948 Guarea rhopalocarpa Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13087.2 Pteridium aquilinum (l.) kuhn var. latiusculum (desv.) unaerw Varieties Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7952 Commelina communis Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15211 Eriogonum brevicaule Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14654 Rhododendron ledebourii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10948 Guarea rhopalocarpa Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5050 Galium triflorum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO863 Rhaphidophora decursiva Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14315 Conostylis setosa Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8723 Ophiostoma piliferum Species Ophiostomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1776 Attalea excelsa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13317 Geigeria acaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7952 Commelina communis Species Commelinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12472 Buddleja davidii Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15590 Peperomia tetraphylla Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15080 Larix kamtschatica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2059 Lactuca denticulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22224 Caragana jubata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO716 Greenwayodendron oliveri Species Annonaceae 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 NPC279098 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 NPC279098 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