Natural Product: NPC475209

Natural Product IDNPC475209
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Tauroside H1
IUPAC Name [(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl] (4aR,5R,6aS,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2S,3R,4S,5S)-4,5-dihydroxy-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-5-hydroxy-2,2,6a,9,9,12a-hexamethyl-3,4,5,6,6a,6b,7,8,8a,10,11,12,13,14b-tetradecahydro-1H-picene-4a-carboxylate
Synonyms Tauroside H1
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL501058
PubChem CID 44559149
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 ZEZRJEPDVLDYDU-FEOFZAIJSA-N
Standard InCHI InChI=1S/C58H94O26/c1-22-34(62)38(66)42(70)49(77-22)82-46-29(19-59)79-48(45(73)41(46)69)76-21-30-37(65)40(68)44(72)51(80-30)84-53(74)58-16-15-54(3,4)17-27(58)26-10-9-24-25(57(26,8)18-32(58)61)11-12-31-55(5,6)33(13-14-56(24,31)7)81-52-47(36(64)28(60)20-75-52)83-50-43(71)39(67)35(63)23(2)78-50/h10,22-25,27-52,59-73H,9,11-21H2,1-8H3/t22-,23-,24-,25+,27-,28-,29+,30+,31-,32+,33-,34-,35-,36-,37+,38+,39+,40-,41+,42+,43+,44+,45+,46+,47+,48+,49-,50-,51-,52-,56+,57-,58+/m0/s1
SMILES OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OC(=O)[C@@]34CCC(C[C@H]4C4=CC[C@H]5[C@H]([C@@]4(C[C@H]3O)C)CC[C@@H]3[C@]5(C)CC[C@@H](C3(C)C)O[C@@H]3OC[C@@H]([C@@H]([C@H]3O[C@@H]3O[C@@H](C)[C@@H]([C@H]([C@H]3O)O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1206.6 Volume:   1149.432
?
Van der Waals volume.
Dense:   1.05 LogP:   0.844
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.509
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.32
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The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   57.0
TPSA:   412.82
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Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   15.0 Rings:   10.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.053 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.282 Fsp3:   0.948
MCE-18:   215.327
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.717 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.315 Promiscuous compounds:   0.104

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.494 MDCK Permeability:   -4.987
Pgp-inhibitor:   0.0 Pgp-substrate:   0.849
PAMPA:   1.0
?
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):   0.996
20% Bioavailability (F20%):   0.814 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.024 MRP1:   0.003
Plasma Protein Binding (PPB):   54.126% Volume Distribution (VD):   -0.274
Fu: 24.863%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 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:   0.898
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.945
HLM stability:   0.024
?
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):  -0.844 Half-life (T1/2):  5.533

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.014
Human Hepatotoxicity (H-HT):  0.565 Drug-induced Liver Injury (DILI):  0.975
AMES Toxicity:  0.97 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.003 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.613 Drug-induced Nephrotoxicity:  0.996
Genotoxicity:  0.278 RPMI-8226 Immunitoxicity:  0.477
A549 Cytotoxicity:  0.921 Hek293 Cytotoxicity:  0.452
BCF:   1.778
?
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:   3.782
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.273
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.452
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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
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. leaf n.a. PMID[11816040]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. PMID[17125224]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. Barks Iksan, Chunbuk, Korea n.a. PMID[3127544]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]

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
NPT2797 Individual protein Pancreatic lipase Homo sapiens Inhibition = 38.3 % PMID[12828466]

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 NPC475209 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
0.7317 Intermediate Similarity NPC220160
0.7009 Intermediate Similarity NPC60557
0.7009 Intermediate Similarity NPC67857
0.6833 Remote Similarity NPC135904
0.6752 Remote Similarity NPC473826
0.6694 Remote Similarity NPC309907
0.6535 Remote Similarity NPC236638
0.6535 Remote Similarity NPC294453
0.6446 Remote Similarity NPC76972
0.6446 Remote Similarity NPC469782
0.6446 Remote Similarity NPC204414
0.6406 Remote Similarity NPC305981
0.6357 Remote Similarity NPC261506
0.6357 Remote Similarity NPC4328
0.6341 Remote Similarity NPC165204
0.625 Remote Similarity NPC295823
0.625 Remote Similarity NPC174720
0.625 Remote Similarity NPC41061
0.625 Remote Similarity NPC475467
0.625 Remote Similarity NPC227551
0.625 Remote Similarity NPC475514
0.6047 Remote Similarity NPC286457
0.6045 Remote Similarity NPC102505
0.6045 Remote Similarity NPC488514
0.6031 Remote Similarity NPC202828
0.6031 Remote Similarity NPC119592
0.6017 Remote Similarity NPC164389
0.597 Remote Similarity NPC250247
0.5968 Remote Similarity NPC114287
0.5938 Remote Similarity NPC488560
0.5923 Remote Similarity NPC110633
0.5923 Remote Similarity NPC13998
0.5878 Remote Similarity NPC258617
0.5865 Remote Similarity NPC309223
0.5865 Remote Similarity NPC298034
0.5865 Remote Similarity NPC71065
0.5833 Remote Similarity NPC63159
0.5833 Remote Similarity NPC43550
0.5806 Remote Similarity NPC104137
0.5806 Remote Similarity NPC26626
0.5758 Remote Similarity NPC470876
0.575 Remote Similarity NPC488526
0.5748 Remote Similarity NPC123522
0.5736 Remote Similarity NPC475160
0.5736 Remote Similarity NPC283417
0.5736 Remote Similarity NPC200049
0.5736 Remote Similarity NPC473714
0.5726 Remote Similarity NPC241909
0.5725 Remote Similarity NPC21691
0.5659 Remote Similarity NPC155410
0.5634 Remote Similarity NPC489208
0.5625 Remote Similarity NPC79643
0.5597 Remote Similarity NPC161717
0.5583 Remote Similarity NPC112352
0.5564 Remote Similarity NPC473452
0.5538 Remote Similarity NPC123199
0.553 Remote Similarity NPC85154
0.553 Remote Similarity NPC481080
0.5508 Remote Similarity NPC475296
0.5496 Remote Similarity NPC100639
0.5489 Remote Similarity NPC476068
0.5441 Remote Similarity NPC136768
0.5429 Remote Similarity NPC489209
0.5426 Remote Similarity NPC475287
0.5425 Remote Similarity NPC469776
0.5414 Remote Similarity NPC4749
0.541 Remote Similarity NPC104071
0.5401 Remote Similarity NPC302543
0.539 Remote Similarity NPC8524
0.5373 Remote Similarity NPC57484
0.5368 Remote Similarity NPC65105
0.5366 Remote Similarity NPC102439
0.5352 Remote Similarity NPC33012
0.5324 Remote Similarity NPC224381
0.5323 Remote Similarity NPC148417
0.5321 Remote Similarity NPC32723
0.5287 Remote Similarity NPC481323
0.5287 Remote Similarity NPC469778
0.5267 Remote Similarity NPC192600
0.5263 Remote Similarity NPC480423
0.525 Remote Similarity NPC474589
0.5238 Remote Similarity NPC64715
0.522 Remote Similarity NPC135334
0.5217 Remote Similarity NPC481081
0.5208 Remote Similarity NPC480421
0.5207 Remote Similarity NPC480420
0.5188 Remote Similarity NPC481324
0.5156 Remote Similarity NPC481079
0.5126 Remote Similarity NPC1046
0.512 Remote Similarity NPC232237
0.5079 Remote Similarity NPC105800
0.5077 Remote Similarity NPC481078
0.5061 Remote Similarity NPC295941
0.5038 Remote Similarity NPC815
0.5036 Remote Similarity NPC293330
0.5036 Remote Similarity NPC237191
0.5035 Remote Similarity NPC70809
0.5032 Remote Similarity NPC469775
0.5032 Remote Similarity NPC485563

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC475209 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