Structure

Physi-Chem Properties

Molecular Weight:  272.07
Volume:  267.823
LogP:  2.276
LogD:  2.328
LogS:  -3.684
# Rotatable Bonds:  1
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.742
Synthetic Accessibility Score:  2.95
Fsp3:  0.133
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.679
MDCK Permeability:  1.2298693945922423e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.068
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.822
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.072
Plasma Protein Binding (PPB):  76.78925323486328%
Volume Distribution (VD):  0.615
Pgp-substrate:  23.050548553466797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.939
CYP1A2-substrate:  0.221
CYP2C19-inhibitor:  0.68
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.698
CYP2C9-substrate:  0.949
CYP2D6-inhibitor:  0.801
CYP2D6-substrate:  0.837
CYP3A4-inhibitor:  0.95
CYP3A4-substrate:  0.148

ADMET: Excretion

Clearance (CL):  17.564
Half-life (T1/2):  0.869

ADMET: Toxicity

hERG Blockers:  0.103
Human Hepatotoxicity (H-HT):  0.247
Drug-inuced Liver Injury (DILI):  0.742
AMES Toxicity:  0.107
Rat Oral Acute Toxicity:  0.698
Maximum Recommended Daily Dose:  0.918
Skin Sensitization:  0.929
Carcinogencity:  0.606
Eye Corrosion:  0.054
Eye Irritation:  0.928
Respiratory Toxicity:  0.71

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

  Natural Product: NPC264083

Natural Product ID:  NPC264083
Common Name*:   OVSYWZXDPOVKQU-AWEZNQCLSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OVSYWZXDPOVKQU-AWEZNQCLSA-N
Standard InCHI:  InChI=1S/C15H12O5/c16-9-1-2-12-13(19)7-14(20-15(12)6-9)8-3-10(17)5-11(18)4-8/h1-6,14,16-18H,7H2/t14-/m0/s1
SMILES:  c1cc2C(=O)C[C@@H](c3cc(cc(c3)O)O)Oc2cc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

*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
NPO25111 Streptomyces tanashiensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)84249-0]
NPO24121 Vernoniopsis caudata n.a. n.a. n.a. n.a. n.a. n.a. PMID[15921436]
NPO20815 Lindera fruticosa Species Lauraceae Eukaryota roots n.a. n.a. PMID[16724860]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21123068]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[26509914]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28522265]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[29641206]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22713 Aquilegia flabellata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23948 Serratia plymuthica Species Yersiniaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20936 Arecastrum romanzoffianum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21683 Selaginella lepidophylla Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14448 Laurencia venusta Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22722 Ranunculus japonicus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21787 Betula pubescens Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23843 Clerodendrum grayi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18589 Allopora californica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16184 Asclepias asperula Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24560 Ricinus communis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24776 Euryops jacksonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21121 Ips japonicus Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20362 Ruta montana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16971 Sparassis crispa Species Sparassidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23158 Penicillium carminoviolaceum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23445 Vernonia triflosculosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23676 Fleroya rubrostipulata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13388 Lithophyllum incrustans Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24121 Vernoniopsis caudata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23376 Genista aetnensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17668 Artemisia gmelinii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20815 Lindera fruticosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25111 Streptomyces tanashiensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24411 Pentaspadon motleyi Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20226 Artemisia filatovae 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
NPT83 Cell Line MCF7 Homo sapiens GI = 13.0 % PMID[28522265]
NPT660 Cell Line SW480 Homo sapiens GI = 4.0 % PMID[28522265]
NPT65 Cell Line HepG2 Homo sapiens GI = 0.0 % PMID[28522265]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 15.0 % PMID[28522265]
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens Inhibition = 2.0 % PMID[28522265]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens FC = 1.54 n.a. PMID[28835349]
NPT2 Others Unspecified Inhibition = 1.0 % PMID[28522265]
NPT2 Others Unspecified Inhibition = 12.0 % PMID[28522265]

☑ 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 NPC264083 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 NPC264083 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