Natural Product: NPC330817

Natural Product IDNPC330817
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Naringenin 7-o-glucoside
IUPAC Name n.a.
Synonyms
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: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 DLIKSSGEMUFQOK-RGHIGTIISA-N
Standard InCHI InChI=1S/C21H22O10/c22-8-16-18(26)19(27)20(28)21(31-16)29-11-5-12(24)17-13(25)7-14(30-15(17)6-11)9-1-3-10(23)4-2-9/h1-6,14,16,18-24,26-28H,7-8H2/t14?,16-,18-,19+,20-,21-/m1/s1
SMILES C1C(OC2=CC(=CC(=C2C1=O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)C4=CC=C(C=C4)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   434.12 Volume:   406.993
?
Van der Waals volume.
Dense:   1.067 LogP:   0.71
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.185
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.086
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   166.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   6.0 Rings:   4.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.385 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.002 Fsp3:   0.381
MCE-18:   87.069
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.645 Fluc inhibitor:   0.405
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.254
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.456
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.267 Promiscuous compounds:   0.232

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.545 MDCK Permeability:   -4.981
Pgp-inhibitor:   0.044 Pgp-substrate:   0.153
PAMPA:   0.978
?
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):   0.112
20% Bioavailability (F20%):   0.003 30% Bioavailability (F30%):   0.983
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.188
Plasma Protein Binding (PPB):   85.176% Volume Distribution (VD):   -0.114
Fu: 13.947%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.982
BSEP inhibitor:   0.065

ADMET: Metabolism

CYP1A2-inhibitor:   0.007 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.01
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.005
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.027
HLM stability:   0.197
?
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):  3.145 Half-life (T1/2):  3.399

ADMET: Toxicity

hERG Blockers:  0.047 hERG Blockers (10um):  0.17
Human Hepatotoxicity (H-HT):  0.825 Drug-induced Liver Injury (DILI):  0.9
AMES Toxicity:  0.933 Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.068 Skin Sensitization:  0.992
Carcinogencity:  0.338 Eye Corrosion:  0.0
Eye Irritation:  0.378 Respiratory Toxicity:  0.029
Drug-induced Neurotoxicity:  0.023 Ototoxicity:  0.939
Hematotoxicity:  0.301 Drug-induced Nephrotoxicity:  0.886
Genotoxicity:  0.866 RPMI-8226 Immunitoxicity:  0.126
A549 Cytotoxicity:  0.512 Hek293 Cytotoxicity:  0.644
BCF:   0.45
?
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:   3.033
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.477
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.663
?
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
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jplph.2011.12.019]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Antalya and Mugla Provinces, Turkey 200-Aug DOI[10.1016/j.scienta.2010.10.027]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1093/jxb/erx356]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Cork, Ireland n.a. PMID[15223592]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[36986275]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[37980871]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10029 Prunus dulcis Species Rosaceae 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. Seeds 0.16125 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]
NPO31303 Solanum lycopersicum n.a. n.a. 0.135 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]

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 NPC330817 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
1.0 High Similarity NPC39351
0.8615 High Similarity NPC97052
0.8507 High Similarity NPC29830
0.8485 Intermediate Similarity NPC219163
0.8143 Intermediate Similarity NPC236934
0.7571 Intermediate Similarity NPC206378
0.7429 Intermediate Similarity NPC26195
0.7391 Intermediate Similarity NPC169248
0.7391 Intermediate Similarity NPC72649
0.7179 Intermediate Similarity NPC142860
0.7179 Intermediate Similarity NPC152538
0.7179 Intermediate Similarity NPC246469
0.7179 Intermediate Similarity NPC89088
0.7051 Intermediate Similarity NPC271270
0.7042 Intermediate Similarity NPC170475
0.6986 Remote Similarity NPC181014
0.6944 Remote Similarity NPC471457
0.6709 Remote Similarity NPC105283
0.6575 Remote Similarity NPC163191
0.6517 Remote Similarity NPC321916
0.64 Remote Similarity NPC106625
0.625 Remote Similarity NPC329203
0.625 Remote Similarity NPC222342
0.6235 Remote Similarity NPC168789
0.619 Remote Similarity NPC291124
0.619 Remote Similarity NPC131157
0.6164 Remote Similarity NPC99233
0.6145 Remote Similarity NPC97285
0.6133 Remote Similarity NPC308265
0.6119 Remote Similarity NPC23084
0.6071 Remote Similarity NPC43587
0.5934 Remote Similarity NPC318119
0.589 Remote Similarity NPC121001
0.5875 Remote Similarity NPC479540
0.5823 Remote Similarity NPC5778
0.5747 Remote Similarity NPC105095
0.5747 Remote Similarity NPC177731
0.5747 Remote Similarity NPC725
0.573 Remote Similarity NPC67134
0.5714 Remote Similarity NPC45400
0.5714 Remote Similarity NPC259182
0.5714 Remote Similarity NPC603902
0.5632 Remote Similarity NPC44328
0.5632 Remote Similarity NPC79056
0.5625 Remote Similarity NPC300537
0.5568 Remote Similarity NPC293629
0.5556 Remote Similarity NPC472381
0.5556 Remote Similarity NPC472383
0.5526 Remote Similarity NPC57587
0.5479 Remote Similarity NPC199335
0.5444 Remote Similarity NPC47140
0.5422 Remote Similarity NPC259834
0.5405 Remote Similarity NPC190217
0.5385 Remote Similarity NPC261254
0.5375 Remote Similarity NPC149244
0.5375 Remote Similarity NPC225445
0.5316 Remote Similarity NPC88484
0.5312 Remote Similarity NPC483821
0.5312 Remote Similarity NPC142319
0.527 Remote Similarity NPC477240
0.5224 Remote Similarity NPC32441
0.5224 Remote Similarity NPC6407
0.5224 Remote Similarity NPC79943
0.5224 Remote Similarity NPC545184
0.5217 Remote Similarity NPC214454
0.519 Remote Similarity NPC271479
0.5185 Remote Similarity NPC472353
0.5185 Remote Similarity NPC257963
0.5181 Remote Similarity NPC477502
0.5152 Remote Similarity NPC483820
0.5147 Remote Similarity NPC150648
0.5139 Remote Similarity NPC214910
0.5132 Remote Similarity NPC479374
0.5104 Remote Similarity NPC241196
0.5072 Remote Similarity NPC73028
0.5072 Remote Similarity NPC145900
0.5065 Remote Similarity NPC604892
0.5063 Remote Similarity NPC148273
0.506 Remote Similarity NPC472320
0.5056 Remote Similarity NPC472876

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC330817 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
0.5632 Remote Similarity NPD7074 Phase 3
0.5224 Remote Similarity NPD1552 Clinical (unspecified phase)

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