Natural Product: NPC491254

Natural Product IDNPC491254
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (+)-Catechin 3-O-gallate
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:0000337] Flavans
          • [CHEMONTID:0003012] Flavan-3-ols
            • [CHEMONTID:0001584] Catechins
              • [CHEMONTID:0001587] Catechin gallates

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 GNXIIYFUGQWDJG-UHFFFAOYSA-N
Standard InCHI InChI=1S/C22H18O10/c23-11-6-14(25)12-8-17(28)21(31-18(12)7-11)9-1-2-13(24)19(5-9)32-22(30)10-3-15(26)20(29)16(27)4-10/h1-7,17,21,23-29H,8H2
SMILES C1C(C(OC2=CC(=CC(=C21)O)O)C3=CC(=C(C=C3)O)OC(=O)C4=CC(=C(C(=C4)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   442.09 Volume:   416.38
?
Van der Waals volume.
Dense:   1.062 LogP:   1.423
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.547
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.389
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   177.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.181 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.586 Fsp3:   0.136
MCE-18:   84.24
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.801 Fluc inhibitor:   0.431
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.698
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.715
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.484 Promiscuous compounds:   0.785

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.548 MDCK Permeability:   -4.933
Pgp-inhibitor:   0.0 Pgp-substrate:   0.028
PAMPA:   0.98
?
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%):   0.931 30% Bioavailability (F30%):   0.994
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.999
Plasma Protein Binding (PPB):   94.024% Volume Distribution (VD):   -0.034
Fu: 7.269%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.112
OATP1B3 inhibitor:   0.899 BCRP inhibitor:   0.71
BSEP inhibitor:   0.034

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.12 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.514
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.405
HLM stability:   0.0
?
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):  8.893 Half-life (T1/2):  2.173

ADMET: Toxicity

hERG Blockers:  0.09 hERG Blockers (10um):  0.876
Human Hepatotoxicity (H-HT):  0.223 Drug-induced Liver Injury (DILI):  0.454
AMES Toxicity:  0.507 Rat Oral Acute Toxicity:  0.353
Maximum Recommended Daily Dose:  0.772 Skin Sensitization:  0.996
Carcinogencity:  0.252 Eye Corrosion:  0.001
Eye Irritation:  0.959 Respiratory Toxicity:  0.349
Drug-induced Neurotoxicity:  0.002 Ototoxicity:  0.911
Hematotoxicity:  0.004 Drug-induced Nephrotoxicity:  0.007
Genotoxicity:  0.955 RPMI-8226 Immunitoxicity:  0.007
A549 Cytotoxicity:  0.968 Hek293 Cytotoxicity:  0.654
BCF:   0.71
?
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:   3.334
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.476
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.97
?
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
NPO25322.1 Matricaria recutita Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22682202]
NPO25322.1 Matricaria recutita Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38843799]
NPO25322.1 Matricaria recutita Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39796439]
NPO25322.1 Matricaria recutita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
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]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25322.1 Matricaria recutita Species Asteraceae 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 n.a. n.a. Database[Phenol-Explorer]
NPO25322.1 Matricaria recutita Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25322.1 Matricaria recutita Species Asteraceae 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
NPO17752 Mentha X piperita n.a. n.a. 0.45 n.a. n.a. mg/100mL Database [Phenol-Explorer]
NPO25322.1 Matricaria recutita n.a. n.a. 0.09 n.a. n.a. mg/100mL 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 NPC491254 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 NPC308402
0.7937 Intermediate Similarity NPC9636
0.7213 Intermediate Similarity NPC16435
0.6406 Remote Similarity NPC171932
0.6333 Remote Similarity NPC268266
0.6333 Remote Similarity NPC42760
0.6333 Remote Similarity NPC220825
0.6333 Remote Similarity NPC268342
0.6129 Remote Similarity NPC261619
0.6129 Remote Similarity NPC61477
0.6129 Remote Similarity NPC78770
0.6129 Remote Similarity NPC219876
0.6129 Remote Similarity NPC126029
0.6129 Remote Similarity NPC15658
0.6066 Remote Similarity NPC207179
0.6066 Remote Similarity NPC167571
0.6066 Remote Similarity NPC278552
0.6 Remote Similarity NPC289990
0.5846 Remote Similarity NPC61946
0.5676 Remote Similarity NPC28440
0.56 Remote Similarity NPC603291
0.5556 Remote Similarity NPC605048
0.5385 Remote Similarity NPC47398
0.5385 Remote Similarity NPC234333
0.5385 Remote Similarity NPC260898
0.5132 Remote Similarity NPC603842
0.507 Remote Similarity NPC326037
0.507 Remote Similarity NPC13858
0.5068 Remote Similarity NPC38779
0.5068 Remote Similarity NPC114179
0.5068 Remote Similarity NPC68324
0.5068 Remote Similarity NPC289322
0.5068 Remote Similarity NPC156818
0.5068 Remote Similarity NPC160512
0.506 Remote Similarity NPC135021

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC491254 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
0.6129 Remote Similarity NPD1612 Clinical (unspecified phase)
0.6129 Remote Similarity NPD1613 Phase 4
0.5114 Remote Similarity NPD7993 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