Natural Product: NPC205613

Natural Product IDNPC205613
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YNHIXLNNNNXLFF-YENJAGDHSA-N
IUPAC Name n.a.
Synonyms epicatechin-(4beta->8)-epicatechin-(4beta->8)-parameritannin A-1
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1213880
PubChem CID 46919853
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 YNHIXLNNNNXLFF-YENJAGDHSA-N
Standard InCHI InChI=1S/C90H72O36/c91-33-19-49(106)59-57(21-33)120-80(28-2-8-37(94)44(101)14-28)75(115)66(59)62-52(109)25-53(110)63-67(76(116)81(122-85(62)63)29-3-9-38(95)45(102)15-29)64-54(111)26-55(112)65-69(78(118)82(123-86(64)65)30-4-10-39(96)46(103)16-30)72-74(114)71-68(61-51(108)24-42(99)35-23-56(113)79(121-84(35)61)27-1-7-36(93)43(100)13-27)77(117)83(31-5-11-40(97)47(104)17-31)124-87(71)73-70-60-50(107)20-34(92)22-58(60)125-90(89(70)119,126-88(72)73)32-6-12-41(98)48(105)18-32/h1-22,24-26,56,66-70,75-83,89,91-119H,23H2/t56-,66-,67-,68+,69-,70-,75-,76-,77-,78-,79-,80-,81-,82-,83-,89-,90+/m1/s1
SMILES Oc1cc(O)c2c(c1)O[C@@]1([C@@H]([C@H]2c2c(O1)c([C@@H]1[C@@H](O)[C@H](Oc3c1c(O)cc(c3[C@@H]1[C@@H](O)[C@H](Oc3c1c(O)cc(c3[C@@H]1[C@@H](O)[C@H](Oc3c1c(O)cc(c3)O)c1ccc(c(c1)O)O)O)c1ccc(c(c1)O)O)O)c1ccc(c(c1)O)O)c(c1c2O[C@H](c2ccc(c(c2)O)O)[C@@H]([C@H]1c1c(O)cc(c2c1O[C@@H]([C@@H](C2)O)c1ccc(c(c1)O)O)O)O)O)O)c1ccc(c(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1728.38 Volume:   1624.158
?
Van der Waals volume.
Dense:   1.064 LogP:   0.91
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.08
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -6.18
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   105.0
TPSA:   651.28
?
Topological Polar Surface Area.
H-Bond Acceptor:   36.0
H-Bond Donor:   29.0 Rings:   19.0
Heavy Atoms:   36.0

MedChem Properties

QED Drug-Likeness Score:   0.057 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.72 Fsp3:   0.2
MCE-18:   410.0
?
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:   Accepted BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.999 Fluc inhibitor:   0.042
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.307
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.662
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.633 Promiscuous compounds:   0.125

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -9.976 MDCK Permeability:   -4.299
Pgp-inhibitor:   0.0 Pgp-substrate:   0.003
PAMPA:   0.001
?
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):   0.0
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   85.749% Volume Distribution (VD):   0.655
Fu: 11.298%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
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):  6.739 Half-life (T1/2):  13.442

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.992
Human Hepatotoxicity (H-HT):  0.998 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.941 Rat Oral Acute Toxicity:  0.994
Maximum Recommended Daily Dose:  1.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.001 Respiratory Toxicity:  1.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.004 Drug-induced Nephrotoxicity:  0.305
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.357
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  1.0
BCF:   0.834
?
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:   4.957
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.142
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.477
?
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
NPO32726 machilus philippinensis Species Lauraceae Eukaryota leaves n.a. n.a. PMID[20568785]

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
NPT2 Others Unspecified n.a. IC50 = 18400.0 nM PMID[26317881]

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 NPC205613 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 NPC212614
0.9865 High Similarity NPC106601
0.9865 High Similarity NPC151474
0.8481 Intermediate Similarity NPC86630
0.8462 Intermediate Similarity NPC147743
0.8462 Intermediate Similarity NPC4809
0.8462 Intermediate Similarity NPC73517
0.8193 Intermediate Similarity NPC159526
0.7568 Intermediate Similarity NPC246202
0.7568 Intermediate Similarity NPC224161
0.7568 Intermediate Similarity NPC46335
0.7568 Intermediate Similarity NPC279406
0.7568 Intermediate Similarity NPC486519
0.75 Intermediate Similarity NPC78074
0.75 Intermediate Similarity NPC478616
0.75 Intermediate Similarity NPC478340
0.75 Intermediate Similarity NPC478339
0.7432 Intermediate Similarity NPC58190
0.7432 Intermediate Similarity NPC108811
0.7432 Intermediate Similarity NPC170103
0.7432 Intermediate Similarity NPC236202
0.7432 Intermediate Similarity NPC262911
0.7432 Intermediate Similarity NPC202742
0.7412 Intermediate Similarity NPC478337
0.7412 Intermediate Similarity NPC478338
0.7215 Intermediate Similarity NPC272552
0.7215 Intermediate Similarity NPC226108
0.7215 Intermediate Similarity NPC322899
0.7 Intermediate Similarity NPC478617
0.6905 Remote Similarity NPC471404
0.6829 Remote Similarity NPC44192
0.6707 Remote Similarity NPC46283
0.6707 Remote Similarity NPC469944
0.6707 Remote Similarity NPC278548
0.6707 Remote Similarity NPC134911
0.6667 Remote Similarity NPC226809
0.6296 Remote Similarity NPC313116
0.6296 Remote Similarity NPC603340
0.6282 Remote Similarity NPC96576
0.6163 Remote Similarity NPC20050
0.6145 Remote Similarity NPC70409
0.6145 Remote Similarity NPC204770
0.6145 Remote Similarity NPC600551
0.6145 Remote Similarity NPC601980
0.6145 Remote Similarity NPC602065
0.6145 Remote Similarity NPC611024
0.6049 Remote Similarity NPC294558
0.6049 Remote Similarity NPC18185
0.6049 Remote Similarity NPC263940
0.6024 Remote Similarity NPC155564
0.6 Remote Similarity NPC600630
0.6 Remote Similarity NPC607896
0.6 Remote Similarity NPC611369
0.5909 Remote Similarity NPC306267
0.5882 Remote Similarity NPC211561
0.5667 Remote Similarity NPC135021
0.5568 Remote Similarity NPC302549
0.5542 Remote Similarity NPC601999
0.5517 Remote Similarity NPC601997
0.5517 Remote Similarity NPC609211
0.5517 Remote Similarity NPC610665
0.5513 Remote Similarity NPC178054
0.5484 Remote Similarity NPC9309
0.5408 Remote Similarity NPC484331
0.5354 Remote Similarity NPC12326
0.5263 Remote Similarity NPC261619
0.5263 Remote Similarity NPC61477
0.5263 Remote Similarity NPC78770
0.5263 Remote Similarity NPC219876
0.5263 Remote Similarity NPC126029
0.5263 Remote Similarity NPC15658
0.5233 Remote Similarity NPC184245
0.5233 Remote Similarity NPC187801
0.5233 Remote Similarity NPC610920
0.5149 Remote Similarity NPC484330
0.5098 Remote Similarity NPC185231

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC205613 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
0.5263 Remote Similarity NPD1612 Clinical (unspecified phase)
0.5263 Remote Similarity NPD1613 Phase 4

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