Natural Product: NPC242260

Natural Product IDNPC242260
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MEDZADGBRDMLGM-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5320291
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

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey MEDZADGBRDMLGM-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H12O7/c1-20-10-3-6-9(4-7(10)16)22-11-5-8(17)15(21-2)14(19)12(11)13(6)18/h3-5,16-17,19H,1-2H3
SMILES COc1cc2c(cc1O)oc1cc(c(c(c1c2=O)O)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   304.06 Volume:   285.403
?
Van der Waals volume.
Dense:   1.065 LogP:   1.642
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.821
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.631
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   17.0
TPSA:   109.36
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.622 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.508 Fsp3:   0.133
MCE-18:   19.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.676 Fluc inhibitor:   0.626
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.793
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.544
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.437 Promiscuous compounds:   0.847

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.118 MDCK Permeability:   -4.784
Pgp-inhibitor:   0.422 Pgp-substrate:   0.654
PAMPA:   0.032
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.029
20% Bioavailability (F20%):   0.091 30% Bioavailability (F30%):   0.538
50% Bioavailability (F50%):   0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.03 MRP1:   0.87
Plasma Protein Binding (PPB):   93.385% Volume Distribution (VD):   -0.447
Fu: 7.847%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.951
OATP1B3 inhibitor:   0.986 BCRP inhibitor:   0.972
BSEP inhibitor:   0.622

ADMET: Metabolism

CYP1A2-inhibitor:   0.97 CYP1A2-substrate:   0.33
CYP2C19-inhibitor:   0.008 CYP2C19-substrate:   0.039
CYP2C9-inhibitor:   0.099 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.911 CYP2D6-substrate:   0.959
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.992
HLM stability:   0.556
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  1.978 Half-life (T1/2):  1.597

ADMET: Toxicity

hERG Blockers:  0.077 hERG Blockers (10um):  0.488
Human Hepatotoxicity (H-HT):  0.418 Drug-induced Liver Injury (DILI):  0.747
AMES Toxicity:  0.615 Rat Oral Acute Toxicity:  0.513
Maximum Recommended Daily Dose:  0.651 Skin Sensitization:  0.705
Carcinogencity:  0.776 Eye Corrosion:  0.578
Eye Irritation:  0.994 Respiratory Toxicity:  0.721
Drug-induced Neurotoxicity:  0.063 Ototoxicity:  0.128
Hematotoxicity:  0.162 Drug-induced Nephrotoxicity:  0.067
Genotoxicity:  0.704 RPMI-8226 Immunitoxicity:  0.071
A549 Cytotoxicity:  0.264 Hek293 Cytotoxicity:  0.477
BCF:   0.752
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   3.411
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.249
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.74
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  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]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota roots n.a. n.a. PMID[16989524]
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]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22060189]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. flower n.a. PMID[22723874]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. rhizome n.a. PMID[22863942]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23371463]
NPO22789 Ecklonia cava Species Lessoniaceae Eukaryota n.a. n.a. n.a. PMID[23647823]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota aerial parts n.a. n.a. PMID[24042007]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flowers Lasa, China n.a. PMID[24621197]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27748595]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[38838926]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39732883]
NPO28551 Centaurium erythraea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28434 Isotropis forrestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28659 Euphorbia terracina Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28205 Isodon setschwanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22789 Ecklonia cava Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28776 Casearia arborea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25755 Haplopappus multifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28239 Indigofera hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28365 Gelasinospora kobi Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24709 Justicia tranquebariensis Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28166 Streptomyces nodosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Bud n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28205 Isodon setschwanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28149 Polygala fallax Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28205 Isodon setschwanensis Species Lamiaceae 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]
NPO25755 Haplopappus multifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28365 Gelasinospora kobi Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28456 Anaptychia obscurata Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6714 Securidaca inappendiculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota 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]
NPO28239 Indigofera hirsuta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28166 Streptomyces nodosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28776 Casearia arborea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28434 Isotropis forrestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24709 Justicia tranquebariensis Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28659 Euphorbia terracina Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21485 Polygala sibirica Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28149 Polygala fallax Species Polygalaceae 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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC242260 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7447 Intermediate Similarity NPC101996
0.6667 Remote Similarity NPC292214
0.6531 Remote Similarity NPC206238
0.6531 Remote Similarity NPC161277
0.6333 Remote Similarity NPC183036
0.62 Remote Similarity NPC39007
0.6078 Remote Similarity NPC603670
0.6078 Remote Similarity NPC609497
0.6 Remote Similarity NPC92564
0.6 Remote Similarity NPC603894
0.5424 Remote Similarity NPC483011
0.54 Remote Similarity NPC55557
0.5303 Remote Similarity NPC262286
0.52 Remote Similarity NPC143903
0.5185 Remote Similarity NPC179183
0.5094 Remote Similarity NPC610896
0.5091 Remote Similarity NPC14786

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC242260 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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