Natural Product: NPC310661

Natural Product IDNPC310661
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Methyl Gallate 4-O-Beta-D-Glucopyranoside
IUPAC Name methyl 3,5-dihydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxybenzoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL485255
PubChem CID 5317705
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic 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 JUPHZGHVZWMVHU-QEGBUVANSA-N
Standard InCHI InChI=1S/C14H18O10/c1-22-13(21)5-2-6(16)12(7(17)3-5)24-14-11(20)10(19)9(18)8(4-15)23-14/h2-3,8-11,14-20H,4H2,1H3/t8-,9-,10+,11-,14+/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2c(O)cc(cc2O)C(=O)OC)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   346.09 Volume:   310.944
?
Van der Waals volume.
Dense:   1.113 LogP:   -0.748
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.106
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.998
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   166.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   6.0 Rings:   2.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.338 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.723 Fsp3:   0.5
MCE-18:   55.619
?
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:   0.504 Fluc inhibitor:   0.097
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.166
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.149
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.306 Promiscuous compounds:   0.76

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.21 MDCK Permeability:   -5.238
Pgp-inhibitor:   0.001 Pgp-substrate:   0.061
PAMPA:   0.823
?
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):   0.002
20% Bioavailability (F20%):   0.37 30% Bioavailability (F30%):   0.921
50% Bioavailability (F50%):   0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.068 MRP1:   1.0
Plasma Protein Binding (PPB):   66.718% Volume Distribution (VD):   -0.41
Fu: 34.602%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.486
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.063
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.023
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.995
HLM stability:   0.98
?
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):  3.171 Half-life (T1/2):  3.188

ADMET: Toxicity

hERG Blockers:  0.016 hERG Blockers (10um):  0.134
Human Hepatotoxicity (H-HT):  0.328 Drug-induced Liver Injury (DILI):  0.851
AMES Toxicity:  0.648 Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.01 Skin Sensitization:  0.991
Carcinogencity:  0.176 Eye Corrosion:  0.0
Eye Irritation:  0.53 Respiratory Toxicity:  0.006
Drug-induced Neurotoxicity:  0.012 Ototoxicity:  0.893
Hematotoxicity:  0.139 Drug-induced Nephrotoxicity:  0.481
Genotoxicity:  0.172 RPMI-8226 Immunitoxicity:  0.081
A549 Cytotoxicity:  0.071 Hek293 Cytotoxicity:  0.092
BCF:   0.226
?
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:   2.592
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.134
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.459
?
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
NPO12848 Carpinus cordata Species Betulaceae Eukaryota stems n.a. n.a. PMID[12350169]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota rhizomes n.a. n.a. PMID[19757853]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. rhizome n.a. PMID[21370894]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota Rhizomes n.a. n.a. PMID[8482946]
NPO12848 Carpinus cordata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7839 Rosa sericea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7839 Rosa sericea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7839 Rosa sericea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12848 Carpinus cordata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7839 Rosa sericea 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

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
NPT1 Others Radical scavenging activity n.a. IC50 > 100.0 ug.mL-1 PMID[12350169]

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 NPC310661 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
0.72 Intermediate Similarity NPC609376
0.6786 Remote Similarity NPC105827
0.66 Remote Similarity NPC484157
0.6102 Remote Similarity NPC599943
0.6 Remote Similarity NPC80098
0.5769 Remote Similarity NPC212729
0.5769 Remote Similarity NPC142319
0.5769 Remote Similarity NPC604498
0.5741 Remote Similarity NPC9248
0.5741 Remote Similarity NPC152722
0.5714 Remote Similarity NPC221090
0.5714 Remote Similarity NPC145900
0.5667 Remote Similarity NPC609351
0.566 Remote Similarity NPC269242
0.5645 Remote Similarity NPC603686
0.5636 Remote Similarity NPC60589
0.5636 Remote Similarity NPC469708
0.56 Remote Similarity NPC228907
0.5593 Remote Similarity NPC19470
0.5556 Remote Similarity NPC192810
0.5556 Remote Similarity NPC294470
0.5536 Remote Similarity NPC12308
0.5517 Remote Similarity NPC40377
0.55 Remote Similarity NPC26080
0.55 Remote Similarity NPC165686
0.55 Remote Similarity NPC481303
0.5484 Remote Similarity NPC607971
0.5484 Remote Similarity NPC609355
0.5441 Remote Similarity NPC191046
0.5397 Remote Similarity NPC100389
0.537 Remote Similarity NPC217854
0.5357 Remote Similarity NPC299144
0.5357 Remote Similarity NPC604439
0.5345 Remote Similarity NPC166168
0.5345 Remote Similarity NPC214454
0.5333 Remote Similarity NPC205054
0.5333 Remote Similarity NPC23084
0.5333 Remote Similarity NPC604356
0.5312 Remote Similarity NPC294166
0.5312 Remote Similarity NPC115022
0.5312 Remote Similarity NPC484156
0.5303 Remote Similarity NPC189115
0.5294 Remote Similarity NPC604833
0.5273 Remote Similarity NPC153149
0.5273 Remote Similarity NPC108455
0.5263 Remote Similarity NPC200092
0.5246 Remote Similarity NPC210015
0.5246 Remote Similarity NPC210478
0.5238 Remote Similarity NPC59324
0.5231 Remote Similarity NPC185778
0.5185 Remote Similarity NPC276195
0.5179 Remote Similarity NPC25817
0.5172 Remote Similarity NPC69513
0.5167 Remote Similarity NPC218685
0.5147 Remote Similarity NPC92054
0.5147 Remote Similarity NPC165720
0.5147 Remote Similarity NPC478798
0.5106 Remote Similarity NPC25305
0.5085 Remote Similarity NPC48863
0.5085 Remote Similarity NPC166040
0.5085 Remote Similarity NPC251981
0.5085 Remote Similarity NPC13745
0.5082 Remote Similarity NPC472024
0.5082 Remote Similarity NPC479028
0.5082 Remote Similarity NPC270849
0.5082 Remote Similarity NPC479031
0.5082 Remote Similarity NPC606892
0.5079 Remote Similarity NPC25292
0.5075 Remote Similarity NPC98777
0.5075 Remote Similarity NPC210192
0.5072 Remote Similarity NPC299435
0.5068 Remote Similarity NPC298847
0.5068 Remote Similarity NPC477502

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC310661 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