Natural Product: NPC198918

Natural Product IDNPC198918
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Pescaprein Xxiv
IUPAC Name n.a.
Synonyms Pescaprein XXIV
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1773740
PubChem CID 52952311
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

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 QXPDXWGBMMLGKK-VZNFXGFUSA-N
Standard InCHI InChI=1S/C70H112O25/c1-10-13-15-16-18-22-30-36-48(72)90-64-63(95-66-54(78)52(76)50(74)40(5)82-66)59(93-69-62(89-49(73)38-37-45-31-26-24-27-32-45)55(79)57(42(7)85-69)91-65(81)39(4)12-3)44(9)86-70(64)92-58-43(8)84-67-56(80)60(58)88-47(71)35-29-23-20-17-19-21-28-34-46(33-25-14-11-2)87-68-61(94-67)53(77)51(75)41(6)83-68/h24,26-27,31-32,37-44,46,50-64,66-70,74-80H,10-23,25,28-30,33-36H2,1-9H3/b38-37+/t39-,40-,41+,42-,43-,44-,46-,50-,51-,52+,53-,54+,55+,56+,57-,58-,59-,60-,61+,62+,63+,64+,66-,67-,68-,69-,70-/m0/s1
SMILES CCCCCCCCCC(=O)O[C@@H]1[C@@H]([C@H]([C@H](C)O[C@H]1O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1OC(=O)CCCCCCCCC[C@H](CCCCC)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](C)O1)O)O)O2)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)[C@@H](C)CC)O)OC(=O)/C=C/c1ccccc1)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)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
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[15730248]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota Leaves Khon Kaen, Thailand 2002-APR PMID[15921434]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota ground entire plants Hainan Province, China 2004-APR PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. aerial part n.a. PMID[21338052]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[31017778]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae 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
NPT2 Others Unspecified n.a. Ratio IC50 = 1.8 n.a. PMID[21338052]

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 NPC198918 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 NPC10121
0.8947 High Similarity NPC35338
0.8947 High Similarity NPC204214
0.8947 High Similarity NPC92283
0.875 High Similarity NPC63404
0.8586 High Similarity NPC10883
0.8454 Intermediate Similarity NPC124878
0.8454 Intermediate Similarity NPC231888
0.8218 Intermediate Similarity NPC290276
0.8091 Intermediate Similarity NPC147032
0.7745 Intermediate Similarity NPC28069
0.7604 Intermediate Similarity NPC162925
0.7579 Intermediate Similarity NPC307400
0.7579 Intermediate Similarity NPC27289
0.7573 Intermediate Similarity NPC77651
0.7396 Intermediate Similarity NPC143421
0.7297 Intermediate Similarity NPC471024
0.7292 Intermediate Similarity NPC477319
0.7273 Intermediate Similarity NPC123204
0.7245 Intermediate Similarity NPC290012
0.7041 Intermediate Similarity NPC472204
0.701 Intermediate Similarity NPC267592
0.7 Intermediate Similarity NPC183888
0.7 Intermediate Similarity NPC259294
0.697 Remote Similarity NPC483170
0.6957 Remote Similarity NPC146380
0.6909 Remote Similarity NPC471025
0.6842 Remote Similarity NPC113745
0.6842 Remote Similarity NPC477320
0.6842 Remote Similarity NPC477323
0.6842 Remote Similarity NPC477325
0.6842 Remote Similarity NPC609436
0.6832 Remote Similarity NPC126685
0.6701 Remote Similarity NPC89843
0.67 Remote Similarity NPC119583
0.6667 Remote Similarity NPC87153
0.6598 Remote Similarity NPC604005
0.6598 Remote Similarity NPC605014
0.6569 Remote Similarity NPC169345
0.6569 Remote Similarity NPC115013
0.63 Remote Similarity NPC477326
0.619 Remote Similarity NPC184915
0.619 Remote Similarity NPC224953
0.6122 Remote Similarity NPC281563
0.6102 Remote Similarity NPC471026
0.6095 Remote Similarity NPC477317
0.6095 Remote Similarity NPC477318
0.6075 Remote Similarity NPC44782
0.6019 Remote Similarity NPC146992
0.6019 Remote Similarity NPC85759
0.6 Remote Similarity NPC22742
0.6 Remote Similarity NPC477346
0.5905 Remote Similarity NPC294748
0.5882 Remote Similarity NPC477331
0.5825 Remote Similarity NPC477344
0.5825 Remote Similarity NPC600446
0.5825 Remote Similarity NPC605013
0.581 Remote Similarity NPC472205
0.5794 Remote Similarity NPC238056
0.5769 Remote Similarity NPC109887
0.5728 Remote Similarity NPC478734
0.566 Remote Similarity NPC173328
0.5636 Remote Similarity NPC269318
0.5619 Remote Similarity NPC478733
0.5545 Remote Similarity NPC472200
0.5524 Remote Similarity NPC158302
0.5514 Remote Similarity NPC297768
0.55 Remote Similarity NPC477350
0.5463 Remote Similarity NPC186992
0.5455 Remote Similarity NPC606819
0.5439 Remote Similarity NPC475241
0.5413 Remote Similarity NPC238264
0.5413 Remote Similarity NPC476087
0.5413 Remote Similarity NPC475667
0.5413 Remote Similarity NPC477345
0.5405 Remote Similarity NPC163409
0.5385 Remote Similarity NPC477349
0.5364 Remote Similarity NPC478732
0.534 Remote Similarity NPC477329
0.5323 Remote Similarity NPC472352
0.5315 Remote Similarity NPC475270
0.5315 Remote Similarity NPC475327
0.5283 Remote Similarity NPC477332
0.5243 Remote Similarity NPC477330
0.5242 Remote Similarity NPC600940
0.5175 Remote Similarity NPC475164
0.5149 Remote Similarity NPC478729
0.5135 Remote Similarity NPC478726
0.513 Remote Similarity NPC478727
0.5096 Remote Similarity NPC477328
0.5043 Remote Similarity NPC478728

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC198918 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