Natural Product: NPC68464

Natural Product IDNPC68464
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
LEXLFIULVWKBPT-ZOGDPUPDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101675598
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 LEXLFIULVWKBPT-ZOGDPUPDSA-N
Standard InCHI InChI=1S/C48H76O19/c1-21-29(51)31(53)34(56)39(63-21)66-37-24(19-49)64-38(36(58)33(37)55)62-20-25-30(52)32(54)35(57)40(65-25)67-42(61)48-16-14-43(2,3)18-23(48)22-8-9-26-44(4)12-11-28(50)47(7,41(59)60)27(44)10-13-46(26,6)45(22,5)15-17-48/h8,21,23-40,49-58H,9-20H2,1-7H3,(H,59,60)/t21-,23-,24+,25+,26+,27+,28+,29-,30+,31+,32-,33+,34+,35+,36+,37+,38+,39-,40-,44+,45+,46+,47-,48-/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[C@H]2C2=CC[C@@H]3[C@@]4(C)CC[C@H]([C@](C)([C@@H]4CC[C@@]3(C)[C@]2(C)CC1)C(=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
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)89267-5]
NPO6003 Halorosellinia oceanica Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[11454459]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[12882150]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15666542]
NPO10814 Ilex latifolia Species Aquifoliaceae Eukaryota n.a. stem n.a. PMID[16252920]
NPO12610 Diospyros dendo Species Ebenaceae Eukaryota n.a. n.a. n.a. PMID[16441080]
NPO3029 Daedalea dickinsii Species Coriolaceae Eukaryota n.a. mycelium n.a. PMID[17986791]
NPO17954 Narcissus tazetta Species Amaryllidaceae Eukaryota n.a. Turkey n.a. PMID[19299148]
NPO6003 Halorosellinia oceanica Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6003 Halorosellinia oceanica Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[21265556]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. trunk bark n.a. PMID[556731]
NPO13061 Balanocarpus zeylanicus n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO17954 Narcissus tazetta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5200 Diphylleia grayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3029 Daedalea dickinsii Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10814 Ilex latifolia Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12781 Schefflera heptaphylla Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6003 Halorosellinia oceanica Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12610 Diospyros dendo Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10670 Bidens frondosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Tuber n.a. n.a. Database[FooDB]
NPO22136 Hedysarum alpinum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota Tubers n.a. Database[FooDB]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10814 Ilex latifolia Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17954 Narcissus tazetta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5200 Diphylleia grayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5200 Diphylleia grayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17954 Narcissus tazetta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10814 Ilex latifolia Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5200 Diphylleia grayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4359 Solanum tuberosum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12019 Orontium japonicum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5200 Diphylleia grayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12781 Schefflera heptaphylla Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15495 Narcissus cantabricus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3568 Myristica dactyloides Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14426 Halictus sexcinctus Species Halictidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10670 Bidens frondosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15944 Primnoa resedaeformis Species Primnoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22136 Hedysarum alpinum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10814 Ilex latifolia Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12836 Mentha javanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13061 Balanocarpus zeylanicus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1349 Zanthoxylum zanthoxyloides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6003 Halorosellinia oceanica Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17954 Narcissus tazetta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12610 Diospyros dendo Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3029 Daedalea dickinsii Species Coriolaceae 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

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 NPC68464 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
0.7921 Intermediate Similarity NPC104071
0.7843 Intermediate Similarity NPC102439
0.7524 Intermediate Similarity NPC609763
0.7248 Intermediate Similarity NPC295823
0.7248 Intermediate Similarity NPC174720
0.7248 Intermediate Similarity NPC241909
0.7248 Intermediate Similarity NPC475467
0.7034 Intermediate Similarity NPC258617
0.6991 Remote Similarity NPC60557
0.6991 Remote Similarity NPC76972
0.6991 Remote Similarity NPC469782
0.6991 Remote Similarity NPC67857
0.6991 Remote Similarity NPC204414
0.693 Remote Similarity NPC192600
0.6916 Remote Similarity NPC469824
0.6881 Remote Similarity NPC146563
0.6814 Remote Similarity NPC75287
0.681 Remote Similarity NPC155410
0.681 Remote Similarity NPC135904
0.6789 Remote Similarity NPC469825
0.6752 Remote Similarity NPC475160
0.6752 Remote Similarity NPC100639
0.6752 Remote Similarity NPC473714
0.6696 Remote Similarity NPC469823
0.6696 Remote Similarity NPC469827
0.6695 Remote Similarity NPC488560
0.6667 Remote Similarity NPC469826
0.6476 Remote Similarity NPC29069
0.6446 Remote Similarity NPC476068
0.6423 Remote Similarity NPC65105
0.6423 Remote Similarity NPC43550
0.6396 Remote Similarity NPC101744
0.6371 Remote Similarity NPC202828
0.6371 Remote Similarity NPC119592
0.6371 Remote Similarity NPC236638
0.6371 Remote Similarity NPC294453
0.6371 Remote Similarity NPC305981
0.6364 Remote Similarity NPC481080
0.6348 Remote Similarity NPC469820
0.6346 Remote Similarity NPC209894
0.632 Remote Similarity NPC261506
0.632 Remote Similarity NPC298034
0.632 Remote Similarity NPC71065
0.632 Remote Similarity NPC4328
0.6262 Remote Similarity NPC48499
0.624 Remote Similarity NPC135849
0.6228 Remote Similarity NPC134835
0.621 Remote Similarity NPC41061
0.621 Remote Similarity NPC227551
0.6195 Remote Similarity NPC148417
0.6174 Remote Similarity NPC73318
0.6172 Remote Similarity NPC250247
0.6033 Remote Similarity NPC165204
0.5893 Remote Similarity NPC295371
0.5868 Remote Similarity NPC300419
0.5826 Remote Similarity NPC473459
0.5812 Remote Similarity NPC601659
0.5806 Remote Similarity NPC470218
0.5776 Remote Similarity NPC63159
0.5766 Remote Similarity NPC11035
0.568 Remote Similarity NPC191827
0.5619 Remote Similarity NPC237503
0.5603 Remote Similarity NPC287269
0.5583 Remote Similarity NPC481079
0.5577 Remote Similarity NPC167383
0.5565 Remote Similarity NPC79643
0.5565 Remote Similarity NPC473343
0.5556 Remote Similarity NPC46665
0.5526 Remote Similarity NPC473373
0.5517 Remote Similarity NPC112352
0.55 Remote Similarity NPC281148
0.55 Remote Similarity NPC114484
0.5496 Remote Similarity NPC481081
0.5462 Remote Similarity NPC475514
0.5439 Remote Similarity NPC235405
0.5424 Remote Similarity NPC251768
0.542 Remote Similarity NPC293330
0.541 Remote Similarity NPC96641
0.541 Remote Similarity NPC163183
0.5391 Remote Similarity NPC249848
0.5391 Remote Similarity NPC107966
0.5385 Remote Similarity NPC110633
0.5378 Remote Similarity NPC475591
0.5378 Remote Similarity NPC236870
0.5378 Remote Similarity NPC235438
0.5373 Remote Similarity NPC220160
0.5373 Remote Similarity NPC51564
0.5366 Remote Similarity NPC187290
0.5354 Remote Similarity NPC123199
0.5349 Remote Similarity NPC487505
0.5339 Remote Similarity NPC109588
0.5308 Remote Similarity NPC57484
0.5303 Remote Similarity NPC161717
0.5294 Remote Similarity NPC40775
0.5267 Remote Similarity NPC469776
0.5267 Remote Similarity NPC469775
0.5263 Remote Similarity NPC136768
0.5263 Remote Similarity NPC32723
0.5263 Remote Similarity NPC469774
0.5259 Remote Similarity NPC224381
0.5259 Remote Similarity NPC478823
0.5259 Remote Similarity NPC150400
0.5254 Remote Similarity NPC192791
0.5242 Remote Similarity NPC473826
0.5238 Remote Similarity NPC475287
0.5229 Remote Similarity NPC481323
0.5229 Remote Similarity NPC469778
0.5214 Remote Similarity NPC473884
0.5214 Remote Similarity NPC157868
0.521 Remote Similarity NPC30735
0.5203 Remote Similarity NPC301449
0.5203 Remote Similarity NPC601290
0.5182 Remote Similarity NPC480417
0.5167 Remote Similarity NPC159309
0.5167 Remote Similarity NPC86222
0.5161 Remote Similarity NPC135334
0.5161 Remote Similarity NPC100925
0.5152 Remote Similarity NPC473645
0.5147 Remote Similarity NPC478824
0.5138 Remote Similarity NPC306746
0.5128 Remote Similarity NPC481324
0.5126 Remote Similarity NPC242840
0.5116 Remote Similarity NPC475209
0.5116 Remote Similarity NPC480419
0.5096 Remote Similarity NPC469777
0.5094 Remote Similarity NPC469772
0.5094 Remote Similarity NPC295941
0.5088 Remote Similarity NPC214484
0.5085 Remote Similarity NPC1876
0.5085 Remote Similarity NPC39211
0.5043 Remote Similarity NPC475516
0.5042 Remote Similarity NPC469946
0.5039 Remote Similarity NPC475899
0.5038 Remote Similarity NPC480418

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC68464 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