Natural Product: NPC114870

Natural Product IDNPC114870
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UODCQSBZHQZMEW-NDVYAFTQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 3081212
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 UODCQSBZHQZMEW-NDVYAFTQSA-N
Standard InCHI InChI=1S/C58H94O26/c1-24-34(64)37(67)41(71)48(77-24)83-46-44(81-47-40(70)35(65)27(62)21-75-47)28(63)22-76-51(46)80-33-11-12-54(4)31(55(33,5)23-61)10-13-57(7)32(54)9-8-25-26-18-53(2,3)14-16-58(26,17-15-56(25,57)6)52(74)84-50-43(73)39(69)45(30(20-60)79-50)82-49-42(72)38(68)36(66)29(19-59)78-49/h8,24,26-51,59-73H,9-23H2,1-7H3/t24-,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-,54-,55?,56+,57+,58-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](CO[C@H]1O[C@H]1CC[C@@]2(C)C(CC[C@]3(C)[C@@H]2CC=C2[C@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)O)C1(C)CO)O)O[C@@H]1[C@@H]([C@H]([C@@H](CO1)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
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2476 Lonicera fulvotomentosa Species Caprifoliaceae 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 NPC114870 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
0.8879 High Similarity NPC100639
0.8077 Intermediate Similarity NPC46665
0.7963 Intermediate Similarity NPC241909
0.7946 Intermediate Similarity NPC155410
0.7838 Intermediate Similarity NPC76972
0.7838 Intermediate Similarity NPC469782
0.7838 Intermediate Similarity NPC204414
0.7563 Intermediate Similarity NPC202828
0.7563 Intermediate Similarity NPC119592
0.75 Intermediate Similarity NPC298034
0.75 Intermediate Similarity NPC71065
0.7478 Intermediate Similarity NPC135904
0.7417 Intermediate Similarity NPC481081
0.7321 Intermediate Similarity NPC295823
0.7321 Intermediate Similarity NPC174720
0.7321 Intermediate Similarity NPC475467
0.729 Intermediate Similarity NPC263756
0.7217 Intermediate Similarity NPC60557
0.7217 Intermediate Similarity NPC67857
0.7083 Intermediate Similarity NPC57484
0.7064 Intermediate Similarity NPC112352
0.7059 Intermediate Similarity NPC488560
0.7049 Intermediate Similarity NPC65105
0.7037 Intermediate Similarity NPC295371
0.6992 Remote Similarity NPC236638
0.6992 Remote Similarity NPC294453
0.6992 Remote Similarity NPC305981
0.6975 Remote Similarity NPC475160
0.6975 Remote Similarity NPC473714
0.6957 Remote Similarity NPC187290
0.6935 Remote Similarity NPC261506
0.6935 Remote Similarity NPC4328
0.6905 Remote Similarity NPC250247
0.6864 Remote Similarity NPC192600
0.686 Remote Similarity NPC481080
0.6829 Remote Similarity NPC41061
0.6829 Remote Similarity NPC227551
0.6818 Remote Similarity NPC161674
0.6726 Remote Similarity NPC68175
0.6667 Remote Similarity NPC476068
0.6667 Remote Similarity NPC481078
0.6667 Remote Similarity NPC469946
0.664 Remote Similarity NPC293330
0.6639 Remote Similarity NPC475287
0.6637 Remote Similarity NPC102439
0.656 Remote Similarity NPC258617
0.6549 Remote Similarity NPC104071
0.6549 Remote Similarity NPC117714
0.6541 Remote Similarity NPC475368
0.6529 Remote Similarity NPC475899
0.6522 Remote Similarity NPC475504
0.6508 Remote Similarity NPC43550
0.6496 Remote Similarity NPC481079
0.648 Remote Similarity NPC473452
0.6435 Remote Similarity NPC475591
0.6435 Remote Similarity NPC63159
0.6435 Remote Similarity NPC236870
0.6423 Remote Similarity NPC471550
0.6379 Remote Similarity NPC297263
0.6372 Remote Similarity NPC213674
0.6355 Remote Similarity NPC256798
0.6348 Remote Similarity NPC10607
0.6341 Remote Similarity NPC123199
0.633 Remote Similarity NPC90856
0.626 Remote Similarity NPC165204
0.625 Remote Similarity NPC235405
0.625 Remote Similarity NPC475516
0.6218 Remote Similarity NPC301449
0.6218 Remote Similarity NPC601290
0.6195 Remote Similarity NPC249848
0.6195 Remote Similarity NPC107966
0.6182 Remote Similarity NPC189884
0.6182 Remote Similarity NPC138334
0.6179 Remote Similarity NPC79643
0.6167 Remote Similarity NPC80986
0.6116 Remote Similarity NPC31838
0.6116 Remote Similarity NPC36831
0.6094 Remote Similarity NPC110633
0.6071 Remote Similarity NPC48499
0.6061 Remote Similarity NPC220160
0.6053 Remote Similarity NPC473373
0.6038 Remote Similarity NPC237503
0.6017 Remote Similarity NPC148417
0.6017 Remote Similarity NPC235438
0.6 Remote Similarity NPC473884
0.5985 Remote Similarity NPC70809
0.597 Remote Similarity NPC480417
0.5969 Remote Similarity NPC286457
0.5965 Remote Similarity NPC139894
0.5954 Remote Similarity NPC136768
0.594 Remote Similarity NPC224381
0.5893 Remote Similarity NPC214484
0.5882 Remote Similarity NPC469777
0.5878 Remote Similarity NPC469775
0.5867 Remote Similarity NPC469774
0.5849 Remote Similarity NPC167383
0.5847 Remote Similarity NPC30735
0.5847 Remote Similarity NPC160415
0.5847 Remote Similarity NPC309714
0.5841 Remote Similarity NPC29069
0.584 Remote Similarity NPC268184
0.5802 Remote Similarity NPC470876
0.5798 Remote Similarity NPC251768
0.5798 Remote Similarity NPC480475
0.5789 Remote Similarity NPC302543
0.5772 Remote Similarity NPC96641
0.5772 Remote Similarity NPC163183
0.5769 Remote Similarity NPC469772
0.5766 Remote Similarity NPC128925
0.5763 Remote Similarity NPC192791
0.5752 Remote Similarity NPC100925
0.5738 Remote Similarity NPC114484
0.5736 Remote Similarity NPC47995
0.5726 Remote Similarity NPC104137
0.5726 Remote Similarity NPC39211
0.5726 Remote Similarity NPC26626
0.5714 Remote Similarity NPC30289
0.5702 Remote Similarity NPC222580
0.5696 Remote Similarity NPC469773
0.5682 Remote Similarity NPC475514
0.5669 Remote Similarity NPC123522
0.5667 Remote Similarity NPC164389
0.5659 Remote Similarity NPC283417
0.5659 Remote Similarity NPC200049
0.5645 Remote Similarity NPC187618
0.5641 Remote Similarity NPC150400
0.5625 Remote Similarity NPC133818
0.5614 Remote Similarity NPC204458
0.561 Remote Similarity NPC281148
0.5597 Remote Similarity NPC477463
0.5575 Remote Similarity NPC209894
0.5573 Remote Similarity NPC85154
0.5565 Remote Similarity NPC1046
0.5556 Remote Similarity NPC815
0.554 Remote Similarity NPC480422
0.5537 Remote Similarity NPC40775
0.5537 Remote Similarity NPC101744
0.5522 Remote Similarity NPC471385
0.552 Remote Similarity NPC480474
0.5519 Remote Similarity NPC469778
0.5517 Remote Similarity NPC475208
0.55 Remote Similarity NPC223301
0.55 Remote Similarity NPC171544
0.5462 Remote Similarity NPC157868
0.5461 Remote Similarity NPC469776
0.5455 Remote Similarity NPC32723
0.5431 Remote Similarity NPC78046
0.542 Remote Similarity NPC470218
0.5419 Remote Similarity NPC481323
0.5417 Remote Similarity NPC473343
0.5417 Remote Similarity NPC76497
0.541 Remote Similarity NPC159309
0.541 Remote Similarity NPC86222
0.5405 Remote Similarity NPC199457
0.5403 Remote Similarity NPC134835
0.5397 Remote Similarity NPC480473
0.5391 Remote Similarity NPC195132
0.5385 Remote Similarity NPC179434
0.5375 Remote Similarity NPC295941
0.5372 Remote Similarity NPC242840
0.5372 Remote Similarity NPC256133
0.536 Remote Similarity NPC104372
0.5357 Remote Similarity NPC68419
0.535 Remote Similarity NPC135334
0.5349 Remote Similarity NPC313110
0.5349 Remote Similarity NPC300419
0.5316 Remote Similarity NPC481324
0.5303 Remote Similarity NPC191827
0.528 Remote Similarity NPC486563
0.528 Remote Similarity NPC79718
0.5268 Remote Similarity NPC306746
0.5238 Remote Similarity NPC73318
0.5227 Remote Similarity NPC251263
0.5227 Remote Similarity NPC480419
0.5203 Remote Similarity NPC109588
0.5203 Remote Similarity NPC472268
0.5197 Remote Similarity NPC218954
0.5185 Remote Similarity NPC21691
0.5175 Remote Similarity NPC477464
0.5167 Remote Similarity NPC174679
0.5167 Remote Similarity NPC279554
0.5167 Remote Similarity NPC59804
0.5161 Remote Similarity NPC11551
0.5161 Remote Similarity NPC473459
0.5149 Remote Similarity NPC473918
0.5147 Remote Similarity NPC480418
0.5141 Remote Similarity NPC489209
0.5135 Remote Similarity NPC297950
0.5124 Remote Similarity NPC58448
0.512 Remote Similarity NPC162574
0.5113 Remote Similarity NPC475209
0.5111 Remote Similarity NPC487505
0.5111 Remote Similarity NPC4749
0.5108 Remote Similarity NPC144644
0.5108 Remote Similarity NPC170407
0.5088 Remote Similarity NPC604133
0.5081 Remote Similarity NPC138057
0.5078 Remote Similarity NPC486564
0.5074 Remote Similarity NPC237191
0.507 Remote Similarity NPC102505

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC114870 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