Natural Product: NPC204414

Natural Product IDNPC204414
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
3Beta-O-[Beta-D-Quinovopyranosyl-(1->2)-Alpha-L-Arabinopyranosyl]Hederagenin 28-O-[Alpha-L-Rhamnopyranosyl(1->4)-Beta-D-Glucopyranosyl-(1->6)-Beta-D-Glucopyranosyl]Ester
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] (4aS,6aR,6aS,6bR,8aR,9R,10S,12aR,14bS)-10-[(2S,3R,4S,5S)-4,5-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL451591
PubChem CID 44575198
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 RYHDIBJJJRNDSX-WHGXSBMGSA-N
Standard InCHI InChI=1S/C59H96O26/c1-24-34(63)38(67)42(71)49(78-24)83-46-29(20-60)80-48(45(74)41(46)70)77-22-30-37(66)40(69)44(73)51(81-30)85-53(75)59-17-15-54(3,4)19-27(59)26-9-10-32-55(5)13-12-33(56(6,23-61)31(55)11-14-58(32,8)57(26,7)16-18-59)82-52-47(36(65)28(62)21-76-52)84-50-43(72)39(68)35(64)25(2)79-50/h9,24-25,27-52,60-74H,10-23H2,1-8H3/t24-,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-,55-,56-,57+,58+,59-/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@@]([C@@]4(CC3)C)(C)CC[C@@H]3[C@]5(C)CC[C@@H]([C@@]3(C)CO)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

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO33015 trevesia palmata Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[10757708]

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
NPT1886 Cell line J774 Mus musculus IC50 = 460.0 nM DOI[10.1039/C2MD00317A]
NPT3470 Cell line WEHI-164 Mus musculus IC50 = 1900.0 nM PMID[18183025]

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 NPC204414 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 NPC76972
1.0 High Similarity NPC469782
0.9216 High Similarity NPC60557
0.9216 High Similarity NPC67857
0.8991 High Similarity NPC202828
0.8991 High Similarity NPC119592
0.8952 High Similarity NPC135904
0.8909 High Similarity NPC298034
0.8909 High Similarity NPC71065
0.8824 High Similarity NPC241909
0.8598 High Similarity NPC155410
0.8519 High Similarity NPC100639
0.8319 Intermediate Similarity NPC236638
0.8319 Intermediate Similarity NPC294453
0.8319 Intermediate Similarity NPC305981
0.8246 Intermediate Similarity NPC261506
0.8246 Intermediate Similarity NPC4328
0.823 Intermediate Similarity NPC65105
0.8142 Intermediate Similarity NPC41061
0.8142 Intermediate Similarity NPC227551
0.8113 Intermediate Similarity NPC295823
0.8113 Intermediate Similarity NPC174720
0.8113 Intermediate Similarity NPC475467
0.8073 Intermediate Similarity NPC192600
0.8 Intermediate Similarity NPC165204
0.7885 Intermediate Similarity NPC102439
0.781 Intermediate Similarity NPC63159
0.7788 Intermediate Similarity NPC104071
0.7759 Intermediate Similarity NPC293330
0.7607 Intermediate Similarity NPC43550
0.7583 Intermediate Similarity NPC250247
0.7524 Intermediate Similarity NPC112352
0.7521 Intermediate Similarity NPC258617
0.7478 Intermediate Similarity NPC488560
0.7434 Intermediate Similarity NPC79643
0.7333 Intermediate Similarity NPC295371
0.7259 Intermediate Similarity NPC469775
0.7241 Intermediate Similarity NPC475160
0.7241 Intermediate Similarity NPC473714
0.7155 Intermediate Similarity NPC123199
0.7143 Intermediate Similarity NPC110633
0.7119 Intermediate Similarity NPC481080
0.7101 Intermediate Similarity NPC469774
0.7073 Intermediate Similarity NPC220160
0.7043 Intermediate Similarity NPC475287
0.695 Remote Similarity NPC100925
0.6937 Remote Similarity NPC475504
0.6917 Remote Similarity NPC476068
0.6917 Remote Similarity NPC57484
0.6853 Remote Similarity NPC469777
0.6792 Remote Similarity NPC48499
0.6763 Remote Similarity NPC469776
0.6754 Remote Similarity NPC481079
0.6712 Remote Similarity NPC469772
0.6696 Remote Similarity NPC148417
0.6694 Remote Similarity NPC481081
0.6667 Remote Similarity NPC224381
0.6638 Remote Similarity NPC481078
0.6622 Remote Similarity NPC469773
0.662 Remote Similarity NPC32723
0.6607 Remote Similarity NPC101744
0.6607 Remote Similarity NPC46665
0.6606 Remote Similarity NPC473373
0.6573 Remote Similarity NPC481323
0.6573 Remote Similarity NPC469778
0.656 Remote Similarity NPC136768
0.6542 Remote Similarity NPC29069
0.6518 Remote Similarity NPC309714
0.6483 Remote Similarity NPC135334
0.6446 Remote Similarity NPC475209
0.6438 Remote Similarity NPC481324
0.6393 Remote Similarity NPC471550
0.6349 Remote Similarity NPC161717
0.6339 Remote Similarity NPC469946
0.6328 Remote Similarity NPC70809
0.632 Remote Similarity NPC473452
0.6293 Remote Similarity NPC134835
0.6267 Remote Similarity NPC295941
0.626 Remote Similarity NPC470218
0.6228 Remote Similarity NPC160415
0.6212 Remote Similarity NPC480422
0.6179 Remote Similarity NPC480419
0.6174 Remote Similarity NPC480475
0.6102 Remote Similarity NPC73318
0.6068 Remote Similarity NPC297263
0.6063 Remote Similarity NPC480418
0.6053 Remote Similarity NPC473343
0.6017 Remote Similarity NPC486563
0.6 Remote Similarity NPC187618
0.5968 Remote Similarity NPC475899
0.5968 Remote Similarity NPC133818
0.595 Remote Similarity NPC31838
0.595 Remote Similarity NPC187290
0.594 Remote Similarity NPC480417
0.5932 Remote Similarity NPC222580
0.5929 Remote Similarity NPC174679
0.5929 Remote Similarity NPC235405
0.5929 Remote Similarity NPC279554
0.5917 Remote Similarity NPC301449
0.5917 Remote Similarity NPC218954
0.5917 Remote Similarity NPC601290
0.5897 Remote Similarity NPC251768
0.5891 Remote Similarity NPC475514
0.5882 Remote Similarity NPC601659
0.5877 Remote Similarity NPC249848
0.5877 Remote Similarity NPC107966
0.5847 Remote Similarity NPC475591
0.5847 Remote Similarity NPC236870
0.5847 Remote Similarity NPC235438
0.5814 Remote Similarity NPC286457
0.5806 Remote Similarity NPC313110
0.5785 Remote Similarity NPC486564
0.5763 Remote Similarity NPC10607
0.5763 Remote Similarity NPC164389
0.5763 Remote Similarity NPC473459
0.5739 Remote Similarity NPC150400
0.5738 Remote Similarity NPC80986
0.5738 Remote Similarity NPC480474
0.5727 Remote Similarity NPC256798
0.5726 Remote Similarity NPC192791
0.5725 Remote Similarity NPC471385
0.5704 Remote Similarity NPC102505
0.5704 Remote Similarity NPC472268
0.5704 Remote Similarity NPC488514
0.5701 Remote Similarity NPC237503
0.569 Remote Similarity NPC473884
0.5678 Remote Similarity NPC109588
0.5678 Remote Similarity NPC30735
0.5641 Remote Similarity NPC161674
0.5634 Remote Similarity NPC297950
0.563 Remote Similarity NPC488526
0.561 Remote Similarity NPC480473
0.5575 Remote Similarity NPC90856
0.5575 Remote Similarity NPC214484
0.5573 Remote Similarity NPC13998
0.5565 Remote Similarity NPC104137
0.5565 Remote Similarity NPC26626
0.5565 Remote Similarity NPC473826
0.5556 Remote Similarity NPC39211
0.5547 Remote Similarity NPC251263
0.5547 Remote Similarity NPC309907
0.553 Remote Similarity NPC470876
0.5522 Remote Similarity NPC309223
0.5517 Remote Similarity NPC139894
0.5517 Remote Similarity NPC475516
0.5517 Remote Similarity NPC59804
0.5514 Remote Similarity NPC167383
0.5512 Remote Similarity NPC123522
0.5508 Remote Similarity NPC263756
0.5504 Remote Similarity NPC191827
0.55 Remote Similarity NPC173859
0.55 Remote Similarity NPC148603
0.5484 Remote Similarity NPC96641
0.5484 Remote Similarity NPC163183
0.5461 Remote Similarity NPC475368
0.5455 Remote Similarity NPC68175
0.5455 Remote Similarity NPC139044
0.5447 Remote Similarity NPC114484
0.5439 Remote Similarity NPC189884
0.5439 Remote Similarity NPC138334
0.5426 Remote Similarity NPC219180
0.5397 Remote Similarity NPC815
0.5385 Remote Similarity NPC283417
0.5385 Remote Similarity NPC200049
0.5385 Remote Similarity NPC56713
0.5379 Remote Similarity NPC21691
0.5378 Remote Similarity NPC76497
0.5378 Remote Similarity NPC213674
0.5372 Remote Similarity NPC473401
0.5345 Remote Similarity NPC475208
0.5333 Remote Similarity NPC223301
0.5333 Remote Similarity NPC171544
0.5329 Remote Similarity NPC472269
0.5328 Remote Similarity NPC471383
0.5328 Remote Similarity NPC162574
0.5323 Remote Similarity NPC281148
0.5323 Remote Similarity NPC104372
0.5323 Remote Similarity NPC276093
0.5317 Remote Similarity NPC36831
0.5315 Remote Similarity NPC489208
0.5289 Remote Similarity NPC471548
0.5285 Remote Similarity NPC488517
0.5267 Remote Similarity NPC480423
0.5263 Remote Similarity NPC209894
0.525 Remote Similarity NPC471547
0.5246 Remote Similarity NPC40775
0.5246 Remote Similarity NPC305267
0.5227 Remote Similarity NPC47995
0.5227 Remote Similarity NPC54636
0.521 Remote Similarity NPC480420
0.5203 Remote Similarity NPC45606
0.5194 Remote Similarity NPC300419
0.5194 Remote Similarity NPC268184
0.5188 Remote Similarity NPC85154
0.5175 Remote Similarity NPC128925
0.5169 Remote Similarity NPC136877
0.5167 Remote Similarity NPC470512
0.5167 Remote Similarity NPC157868
0.5161 Remote Similarity NPC131469

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC204414 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