Natural Product: NPC29830

Natural Product IDNPC29830
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Eriodictyol-7-O-Glucoside
IUPAC Name (2S)-2-(3,4-dihydroxyphenyl)-5-hydroxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL509624
PubChem CID 13254473
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 RAFHNDRXYHOLSH-SFTVRKLSSA-N
Standard InCHI InChI=1S/C21H22O11/c22-7-16-18(27)19(28)20(29)21(32-16)30-9-4-12(25)17-13(26)6-14(31-15(17)5-9)8-1-2-10(23)11(24)3-8/h1-5,14,16,18-25,27-29H,6-7H2/t14-,16+,18+,19-,20+,21+/m0/s1
SMILES OC[C@H]1O[C@@H](Oc2cc3O[C@@H](CC(=O)c3c(c2)O)c2ccc(c(c2)O)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   450.12 Volume:   415.784
?
Van der Waals volume.
Dense:   1.083 LogP:   0.598
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.07
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.208
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   186.37
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.303 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.123 Fsp3:   0.381
MCE-18:   90.552
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.655 Fluc inhibitor:   0.461
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.28
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.64
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.23 Promiscuous compounds:   0.354

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.675 MDCK Permeability:   -5.018
Pgp-inhibitor:   0.011 Pgp-substrate:   0.019
PAMPA:   0.985
?
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):   0.42
20% Bioavailability (F20%):   0.013 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.189
Plasma Protein Binding (PPB):   84.378% Volume Distribution (VD):   -0.18
Fu: 14.118%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.993
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.008 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.006
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.353
HLM stability:   0.31
?
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):  3.802 Half-life (T1/2):  3.972

ADMET: Toxicity

hERG Blockers:  0.025 hERG Blockers (10um):  0.169
Human Hepatotoxicity (H-HT):  0.799 Drug-induced Liver Injury (DILI):  0.925
AMES Toxicity:  0.954 Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.064 Skin Sensitization:  0.999
Carcinogencity:  0.252 Eye Corrosion:  0.0
Eye Irritation:  0.663 Respiratory Toxicity:  0.006
Drug-induced Neurotoxicity:  0.012 Ototoxicity:  0.973
Hematotoxicity:  0.187 Drug-induced Nephrotoxicity:  0.806
Genotoxicity:  0.968 RPMI-8226 Immunitoxicity:  0.082
A549 Cytotoxicity:  0.818 Hek293 Cytotoxicity:  0.33
BCF:   0.542
?
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:   3.144
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.868
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.949
?
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
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Antalya and Mugla Provinces, Turkey 200-Aug DOI[10.1016/j.scienta.2010.10.027]
NPO15592 Swertia punctata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(02)00231-5]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11087602]
NPO15592 Swertia punctata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[12377236]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. stem n.a. PMID[12932124]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[12932124]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Cork, Ireland n.a. PMID[15223592]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19499937]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. PMID[20121165]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20932762]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[36986275]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39419301]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3676 Fusarium sambucinum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8 Buphthalmum salicifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4578 Cystoseira fimbriata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16561 Viscum articulatum Species Viscaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3676 Fusarium sambucinum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4578 Cystoseira fimbriata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14062 Oophaga speciosa Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8 Buphthalmum salicifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO539 Picea vulgaris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15592 Swertia punctata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18048 Phlomis crinita Species Lamiaceae 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
NPO10029 Prunus dulcis n.a. n.a. 3.20 ± 0.10 n.a. n.a. mg/100g PMID[36986275]
NPO10029 Prunus dulcis n.a. n.a. 2.03 ± 0.05 n.a. n.a. mg/100g PMID[36986275]
NPO10029 Prunus dulcis n.a. n.a. 1.08 ± 0.02 n.a. n.a. mg/100g PMID[36986275]
NPO10029 Prunus dulcis n.a. n.a. 0.01 ± 0.00 n.a. n.a. mg/100g PMID[36986275]
NPO17752 Mentha X piperita n.a. n.a. 80.25148 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]
NPO18048 Phlomis crinita Methanolic extract Flowers 0.36 ± 0.01 n.a. n.a. % PMID[39419301]

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
NPT67 Individual protein Cholinesterase Equus caballus Inhibition = -9.51 % PMID[23062825]
NPT66 Individual protein Acetylcholinesterase Electrophorus electricus Inhibition = 25.44 % PMID[23062825]
NPT622 Individual protein Solute carrier organic anion transporter family member 2B1 Homo sapiens Inhibition > 40.0 % PMID[37252098]
NPT622 Individual protein Solute carrier organic anion transporter family member 2B1 Homo sapiens IC50 = 61659.5 nM PMID[37252098]
NPT622 Individual protein Solute carrier organic anion transporter family member 2B1 Homo sapiens Inhibition = 20.0 % PMID[37252098]
NPT622 Individual protein Solute carrier organic anion transporter family member 2B1 Homo sapiens IC50 = 61500.0 nM PMID[37252098]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus IC50 = 41200.0 nM PMID[20121165]
NPT113 Cell line RAW264.7 Mus musculus Activity = 100.0 % PMID[20121165]
NPT1635 Cell line H9c2 Rattus norvegicus EC50 = 38230.0 nM PMID[20932762]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 1.263 mM PMID[12932124]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 212900000.0 nM PMID[20932762]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 7260.0 nM PMID[20932762]
NPT1 Others Radical scavenging activity n.a. ED50 = 63.3 uM PMID[20121165]
NPT1 Others Radical scavenging activity n.a. EC50 = 15600.0 nM PMID[20932762]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Inhibition n.a. n.a. % PMID[34106718]





 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 NPC29830 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
0.8507 High Similarity NPC39351
0.8088 Intermediate Similarity NPC97052
0.7971 Intermediate Similarity NPC219163
0.7917 Intermediate Similarity NPC236934
0.7867 Intermediate Similarity NPC105283
0.7571 Intermediate Similarity NPC163191
0.725 Intermediate Similarity NPC291124
0.725 Intermediate Similarity NPC131157
0.7125 Intermediate Similarity NPC43587
0.6897 Remote Similarity NPC318119
0.6849 Remote Similarity NPC45400
0.6757 Remote Similarity NPC26195
0.6706 Remote Similarity NPC67134
0.6447 Remote Similarity NPC206378
0.6395 Remote Similarity NPC47140
0.6374 Remote Similarity NPC321916
0.6282 Remote Similarity NPC300537
0.6267 Remote Similarity NPC169248
0.6267 Remote Similarity NPC72649
0.619 Remote Similarity NPC142860
0.619 Remote Similarity NPC152538
0.619 Remote Similarity NPC246469
0.619 Remote Similarity NPC89088
0.6184 Remote Similarity NPC170475
0.6104 Remote Similarity NPC471457
0.6071 Remote Similarity NPC271270
0.6026 Remote Similarity NPC149244
0.5977 Remote Similarity NPC105095
0.5977 Remote Similarity NPC177731
0.5977 Remote Similarity NPC725
0.5949 Remote Similarity NPC181014
0.5942 Remote Similarity NPC23084
0.5875 Remote Similarity NPC5778
0.5862 Remote Similarity NPC44328
0.5862 Remote Similarity NPC79056
0.5814 Remote Similarity NPC97285
0.5684 Remote Similarity NPC483821
0.5676 Remote Similarity NPC480158
0.5625 Remote Similarity NPC106625
0.5625 Remote Similarity NPC257963
0.557 Remote Similarity NPC308265
0.5556 Remote Similarity NPC469371
0.5556 Remote Similarity NPC168789
0.5513 Remote Similarity NPC606353
0.5444 Remote Similarity NPC293629
0.5422 Remote Similarity NPC472381
0.5422 Remote Similarity NPC472383
0.5286 Remote Similarity NPC321011
0.5286 Remote Similarity NPC294852
0.5286 Remote Similarity NPC188679
0.5269 Remote Similarity NPC261254
0.525 Remote Similarity NPC160156
0.525 Remote Similarity NPC92565
0.5238 Remote Similarity NPC477502
0.519 Remote Similarity NPC99233
0.5185 Remote Similarity NPC46067
0.5143 Remote Similarity NPC329203
0.5143 Remote Similarity NPC222342
0.5132 Remote Similarity NPC199335
0.5128 Remote Similarity NPC121001
0.507 Remote Similarity NPC214454
0.5065 Remote Similarity NPC190217
0.506 Remote Similarity NPC48640

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC29830 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
0.5862 Remote Similarity NPD7074 Phase 3

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