Natural Product: NPC148417

Natural Product IDNPC148417
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
3-O-Beta-D-Glucopyranosyl-(1->4)-Alpha-L-Arabinopyranosyl Siaresinolic Acid 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] (1S,4aR,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2S,3R,4R,5S)-3,4-dihydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-1-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-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 CHEMBL2430032
PubChem CID 72189232
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 LKXSEJWOAPOCIO-SIOYIREESA-N
Standard InCHI InChI=1S/C59H96O27/c1-23-33(62)37(66)42(71)50(79-23)85-46-26(20-61)81-48(45(74)40(46)69)77-21-27-35(64)39(68)44(73)52(83-27)86-53(76)59-17-15-54(2,3)47(75)32(59)24-9-10-30-56(6)13-12-31(55(4,5)29(56)11-14-58(30,8)57(24,7)16-18-59)84-49-41(70)36(65)28(22-78-49)82-51-43(72)38(67)34(63)25(19-60)80-51/h9,23,25-52,60-75H,10-22H2,1-8H3/t23-,25+,26+,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+,59-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](CO)O[C@H]([C@@H]([C@H]1O)O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)OC(=O)[C@@]12CCC(C)(C)[C@H]([C@H]2C2=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@H](CO1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O)O)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
NPO32682 anemone taipaiensis Species Ranunculaceae Eukaryota rhizomes n.a. n.a. PMID[23992864]
NPO32682 anemone taipaiensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT165 Cell line HeLa Homo sapiens IC50 > 80000.0 nM PMID[23398362]
NPT81 Cell line A549 Homo sapiens IC50 > 80000.0 nM PMID[7623046]
NPT116 Cell line HL-60 Homo sapiens IC50 > 80000.0 nM PMID[22840694]
NPT65 Cell line HepG2 Homo sapiens IC50 > 80000.0 nM PMID[19331379]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 29040.0 nM PMID[23992864]

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 NPC148417 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
0.7838 Intermediate Similarity NPC136768
0.7767 Intermediate Similarity NPC295823
0.7767 Intermediate Similarity NPC174720
0.7767 Intermediate Similarity NPC475467
0.7727 Intermediate Similarity NPC110633
0.7685 Intermediate Similarity NPC475160
0.7685 Intermediate Similarity NPC473714
0.7593 Intermediate Similarity NPC135904
0.7447 Intermediate Similarity NPC128925
0.74 Intermediate Similarity NPC161674
0.7387 Intermediate Similarity NPC481080
0.7321 Intermediate Similarity NPC476068
0.7315 Intermediate Similarity NPC60557
0.7315 Intermediate Similarity NPC67857
0.7245 Intermediate Similarity NPC48499
0.7193 Intermediate Similarity NPC258617
0.7182 Intermediate Similarity NPC165204
0.7155 Intermediate Similarity NPC261506
0.7155 Intermediate Similarity NPC4328
0.7143 Intermediate Similarity NPC488560
0.713 Intermediate Similarity NPC43550
0.7103 Intermediate Similarity NPC241909
0.7069 Intermediate Similarity NPC305981
0.7019 Intermediate Similarity NPC101744
0.6923 Remote Similarity NPC104071
0.6903 Remote Similarity NPC100639
0.6897 Remote Similarity NPC41061
0.6897 Remote Similarity NPC227551
0.6857 Remote Similarity NPC102439
0.6833 Remote Similarity NPC250247
0.6786 Remote Similarity NPC192600
0.6735 Remote Similarity NPC256798
0.6696 Remote Similarity NPC76972
0.6696 Remote Similarity NPC469782
0.6696 Remote Similarity NPC204414
0.6667 Remote Similarity NPC134835
0.6639 Remote Similarity NPC236638
0.6639 Remote Similarity NPC294453
0.6583 Remote Similarity NPC298034
0.6583 Remote Similarity NPC71065
0.6555 Remote Similarity NPC65105
0.6538 Remote Similarity NPC473373
0.6522 Remote Similarity NPC155410
0.6514 Remote Similarity NPC469821
0.6481 Remote Similarity NPC63159
0.6471 Remote Similarity NPC475514
0.6455 Remote Similarity NPC73318
0.6396 Remote Similarity NPC481079
0.6316 Remote Similarity NPC191763
0.6286 Remote Similarity NPC235405
0.6239 Remote Similarity NPC173859
0.6239 Remote Similarity NPC148603
0.6239 Remote Similarity NPC46665
0.623 Remote Similarity NPC481081
0.6226 Remote Similarity NPC249848
0.6226 Remote Similarity NPC107966
0.6216 Remote Similarity NPC601659
0.621 Remote Similarity NPC220160
0.6207 Remote Similarity NPC79643
0.6204 Remote Similarity NPC112352
0.6182 Remote Similarity NPC68175
0.6182 Remote Similarity NPC235438
0.6168 Remote Similarity NPC295371
0.6154 Remote Similarity NPC78046
0.6147 Remote Similarity NPC30735
0.6147 Remote Similarity NPC160415
0.614 Remote Similarity NPC473826
0.6098 Remote Similarity NPC202828
0.6098 Remote Similarity NPC119592
0.6061 Remote Similarity NPC116794
0.6058 Remote Similarity NPC204458
0.6058 Remote Similarity NPC90856
0.6 Remote Similarity NPC29069
0.5966 Remote Similarity NPC123199
0.596 Remote Similarity NPC605954
0.5917 Remote Similarity NPC470218
0.5905 Remote Similarity NPC214484
0.5902 Remote Similarity NPC57484
0.5872 Remote Similarity NPC470512
0.5872 Remote Similarity NPC39211
0.5847 Remote Similarity NPC475287
0.5833 Remote Similarity NPC475516
0.5818 Remote Similarity NPC473343
0.5818 Remote Similarity NPC76497
0.578 Remote Similarity NPC58448
0.5739 Remote Similarity NPC114484
0.5726 Remote Similarity NPC36831
0.5724 Remote Similarity NPC469778
0.5676 Remote Similarity NPC469946
0.5664 Remote Similarity NPC469776
0.5655 Remote Similarity NPC32723
0.5635 Remote Similarity NPC161717
0.5625 Remote Similarity NPC223301
0.5625 Remote Similarity NPC171544
0.562 Remote Similarity NPC470911
0.5616 Remote Similarity NPC481323
0.5614 Remote Similarity NPC470515
0.5603 Remote Similarity NPC281148
0.5603 Remote Similarity NPC104372
0.5583 Remote Similarity NPC268184
0.5581 Remote Similarity NPC224381
0.5575 Remote Similarity NPC109588
0.5565 Remote Similarity NPC222580
0.5563 Remote Similarity NPC295941
0.5546 Remote Similarity NPC470915
0.5545 Remote Similarity NPC108748
0.5541 Remote Similarity NPC135334
0.5526 Remote Similarity NPC40775
0.5526 Remote Similarity NPC10607
0.5526 Remote Similarity NPC251768
0.5526 Remote Similarity NPC480475
0.5512 Remote Similarity NPC293330
0.5508 Remote Similarity NPC80986
0.5504 Remote Similarity NPC70809
0.5478 Remote Similarity NPC475591
0.5478 Remote Similarity NPC236870
0.5463 Remote Similarity NPC189884
0.5463 Remote Similarity NPC138334
0.5462 Remote Similarity NPC481078
0.5462 Remote Similarity NPC187290
0.5446 Remote Similarity NPC1876
0.5446 Remote Similarity NPC157868
0.5439 Remote Similarity NPC309714
0.5431 Remote Similarity NPC470513
0.5431 Remote Similarity NPC297263
0.54 Remote Similarity NPC481324
0.5391 Remote Similarity NPC159309
0.5391 Remote Similarity NPC473459
0.5391 Remote Similarity NPC86222
0.537 Remote Similarity NPC161434
0.536 Remote Similarity NPC54636
0.5354 Remote Similarity NPC286457
0.5351 Remote Similarity NPC192791
0.5351 Remote Similarity NPC75417
0.5333 Remote Similarity NPC31838
0.5323 Remote Similarity NPC475209
0.5321 Remote Similarity NPC269095
0.5319 Remote Similarity NPC45606
0.5315 Remote Similarity NPC136877
0.5304 Remote Similarity NPC137414
0.5299 Remote Similarity NPC470514
0.5294 Remote Similarity NPC301449
0.5294 Remote Similarity NPC601290
0.5285 Remote Similarity NPC123522
0.5263 Remote Similarity NPC469777
0.5259 Remote Similarity NPC164389
0.5246 Remote Similarity NPC114287
0.5238 Remote Similarity NPC47995
0.5238 Remote Similarity NPC469775
0.5235 Remote Similarity NPC469774
0.5229 Remote Similarity NPC47063
0.5194 Remote Similarity NPC470876
0.5189 Remote Similarity NPC187056
0.5189 Remote Similarity NPC137917
0.5189 Remote Similarity NPC606216
0.5189 Remote Similarity NPC607023
0.5185 Remote Similarity NPC480422
0.5182 Remote Similarity NPC473481
0.5172 Remote Similarity NPC287269
0.5169 Remote Similarity NPC469822
0.5169 Remote Similarity NPC257468
0.5161 Remote Similarity NPC469772
0.5146 Remote Similarity NPC473844
0.5143 Remote Similarity NPC237503
0.5135 Remote Similarity NPC1046
0.5132 Remote Similarity NPC100925
0.5128 Remote Similarity NPC473401
0.5124 Remote Similarity NPC480473
0.5124 Remote Similarity NPC470516
0.5124 Remote Similarity NPC480474
0.5096 Remote Similarity NPC167383
0.5096 Remote Similarity NPC469773
0.5094 Remote Similarity NPC37739
0.5088 Remote Similarity NPC173583
0.5085 Remote Similarity NPC258885
0.5082 Remote Similarity NPC104137
0.5082 Remote Similarity NPC26626
0.5079 Remote Similarity NPC219180
0.5079 Remote Similarity NPC251263
0.5076 Remote Similarity NPC309223
0.5048 Remote Similarity NPC46388
0.5043 Remote Similarity NPC471548
0.5042 Remote Similarity NPC146563
0.5039 Remote Similarity NPC470517
0.5039 Remote Similarity NPC471550

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC148417 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