Structure

Physi-Chem Properties

Molecular Weight:  290.08
Volume:  267.409
LogP:  1.25
LogD:  1.534
LogS:  -3.621
# Rotatable Bonds:  0
TPSA:  84.73
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.443
Synthetic Accessibility Score:  6.329
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  3
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.349
MDCK Permeability:  1.7593984011909924e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.038
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.201
Plasma Protein Binding (PPB):  82.73768615722656%
Volume Distribution (VD):  1.002
Pgp-substrate:  16.0740966796875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.055
CYP1A2-substrate:  0.53
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.705
CYP2C9-inhibitor:  0.111
CYP2C9-substrate:  0.053
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.184
CYP3A4-inhibitor:  0.073
CYP3A4-substrate:  0.244

ADMET: Excretion

Clearance (CL):  9.661
Half-life (T1/2):  0.462

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.213
Drug-inuced Liver Injury (DILI):  0.894
AMES Toxicity:  0.184
Rat Oral Acute Toxicity:  0.862
Maximum Recommended Daily Dose:  0.747
Skin Sensitization:  0.529
Carcinogencity:  0.533
Eye Corrosion:  0.025
Eye Irritation:  0.026
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC240563

Natural Product ID:  NPC240563
Common Name*:   JRZGAAFGODYEEA-ATNXOXLHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JRZGAAFGODYEEA-ATNXOXLHSA-N
Standard InCHI:  InChI=1S/C15H14O6/c1-5-9-7-3-6(14(17)18-7)10-11(20-10)12-15(2,21-12)4-8(9)19-13(5)16/h3,7-12H,1,4H2,2H3/t7-,8+,9+,10-,11-,12+,15+/m1/s1
SMILES:  C=C1[C@H]2[C@H]3C=C([C@@H]4[C@H]([C@H]5[C@](C)(C[C@@H]2OC1=O)O5)O4)C(=O)O3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   442282
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO25515 Garcinia speciosa Species Clusiaceae Eukaryota barks n.a. n.a. PMID[15620248]
NPO24708 Mikania micrantha Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19267453]
NPO23707 Sinularia gyrosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[20430633]
NPO23707 Sinularia gyrosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[20499851]
NPO23998 Auxarthron reticulatum Species Onygenaceae Eukaryota n.a. n.a. n.a. PMID[24900275]
NPO6403 Phlegmariurus squarrosus Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[32941036]
NPO9783 Mikania scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28627 Coptis trifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22408 Aconitum polyschistum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25515 Garcinia speciosa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9783 Mikania scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25515 Garcinia speciosa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24950 Eupatorium aschenbornianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22408 Aconitum polyschistum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28627 Coptis trifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9783 Mikania scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25602 Crotalaria barbata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9783 Mikania scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25399 Patrinia intermedia Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25241 Cordyla africana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23866 Anisocycla cymosa Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28627 Coptis trifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24242 Haminoea cymbalum Species Haminoeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25313 Satureja douglasii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25683 Columba livia Species Columbidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6403 Phlegmariurus squarrosus Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25115 Psychotria calocarpa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24142 Cereus ocamponis Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24895 Parmelia springtonensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22408 Aconitum polyschistum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23134 Artemisia kaschgarica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24662 Ulmus laevis Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20331 Aerva tomentosa Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23707 Sinularia gyrosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1827 Morinda elliptica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23998 Auxarthron reticulatum Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25341 Sanango racemosum Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25515 Garcinia speciosa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24708 Mikania micrantha Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24854 Beltrania rhombica Species Beltraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24950 Eupatorium aschenbornianum 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 NPC240563 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 NPC240563 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