Structure

Physi-Chem Properties

Molecular Weight:  258.05
Volume:  250.527
LogP:  2.704
LogD:  2.409
LogS:  -3.326
# Rotatable Bonds:  1
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.655
Synthetic Accessibility Score:  2.259
Fsp3:  0.071
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.905
MDCK Permeability:  1.713946767267771e-05
Pgp-inhibitor:  0.274
Pgp-substrate:  0.033
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.084

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.024
Plasma Protein Binding (PPB):  93.54790496826172%
Volume Distribution (VD):  0.645
Pgp-substrate:  11.408544540405273%

ADMET: Metabolism

CYP1A2-inhibitor:  0.972
CYP1A2-substrate:  0.935
CYP2C19-inhibitor:  0.306
CYP2C19-substrate:  0.121
CYP2C9-inhibitor:  0.676
CYP2C9-substrate:  0.867
CYP2D6-inhibitor:  0.696
CYP2D6-substrate:  0.409
CYP3A4-inhibitor:  0.409
CYP3A4-substrate:  0.178

ADMET: Excretion

Clearance (CL):  2.032
Half-life (T1/2):  0.736

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.048
Drug-inuced Liver Injury (DILI):  0.947
AMES Toxicity:  0.658
Rat Oral Acute Toxicity:  0.157
Maximum Recommended Daily Dose:  0.125
Skin Sensitization:  0.898
Carcinogencity:  0.304
Eye Corrosion:  0.091
Eye Irritation:  0.964
Respiratory Toxicity:  0.331

Download Data

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

  Natural Product: NPC90161

Natural Product ID:  NPC90161
Common Name*:   PVNLFOMDIZUYGA-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PVNLFOMDIZUYGA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H10O5/c1-18-14-8(15)6-10-11(13(14)17)12(16)7-4-2-3-5-9(7)19-10/h2-6,15,17H,1H3
SMILES:  COc1c(cc2c(c(=O)c3ccccc3o2)c1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5316798
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

*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
NPO28551 Centaurium erythraea Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50044a037]
NPO28776 Casearia arborea Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[10843580]
NPO28166 Streptomyces nodosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[15730252]
NPO22789 Ecklonia cava Species Lessoniaceae Eukaryota n.a. n.a. n.a. PMID[18693022]
NPO22789 Ecklonia cava Species Lessoniaceae Eukaryota n.a. n.a. n.a. PMID[19201199]
NPO22789 Ecklonia cava Species Lessoniaceae Eukaryota n.a. n.a. n.a. PMID[23647823]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[24216090]
NPO20441 Glaucium flavum Species Papaveraceae Eukaryota n.a. root n.a. PMID[24317429]
NPO4969 Sesbania bispinosa Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20441 Glaucium flavum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20441 Glaucium flavum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28205 Isodon setschwanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20441 Glaucium flavum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28239 Indigofera hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21581 Polygala arillata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28365 Gelasinospora kobi Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28166 Streptomyces nodosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28776 Casearia arborea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20441 Glaucium flavum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21068 Centaurea sulphurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4969 Sesbania bispinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28456 Anaptychia obscurata Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28205 Isodon setschwanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28434 Isotropis forrestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19599 Pogostemon parviflorus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24709 Justicia tranquebariensis Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25755 Haplopappus multifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28659 Euphorbia terracina Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28515 Campanula kachetica Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14228 Mattfeldanthus nobilis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28551 Centaurium erythraea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22789 Ecklonia cava Species Lessoniaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. PC50 = 81.2 uM PMID[455671]
NPT2 Others Unspecified Inhibition = 24.66 % PMID[455672]
NPT2 Others Unspecified Inhibition = 40.1 % PMID[455672]
NPT741 Individual Protein Tyrosinase Homo sapiens IC50 = 3010.0 nM PMID[455672]
NPT741 Individual Protein Tyrosinase Homo sapiens Inhibition = 99.82 % PMID[455672]

☑ 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 NPC90161 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 NPC90161 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