Natural Product: NPC479045

Natural Product IDNPC479045
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PICHJWVARQFKFP-QWQOFHFFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 PICHJWVARQFKFP-QWQOFHFFSA-N
Standard InCHI InChI=1S/C36H38O14/c1-20(37)45-19-35-27(48-31(40)23-11-13-43-17-23)15-25-28(46-21(2)38)36(35,50-33(25,3)4)34(5,42)16-26(47-30(39)22-9-7-6-8-10-22)29(35)49-32(41)24-12-14-44-18-24/h6-14,17-18,25-29,42H,15-16,19H2,1-5H3/t25-,26+,27-,28-,29+,34+,35-,36+/m1/s1
SMILES CC(=O)OC[C@@]12[C@@H](C[C@@H]3[C@H]([C@@]2([C@](C)(C[C@@H]([C@@H]1OC(=O)c1ccoc1)OC(=O)c1ccccc1)O)OC3(C)C)OC(=O)C)OC(=O)c1ccoc1

  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
NPO3549 Euonymus maackii Species Celastraceae Eukaryota Seeds n.a. n.a. PMID[31713425]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3549 Euonymus maackii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3549 Euonymus maackii Species Celastraceae 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
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 80.8 % PMID[31713425]

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 NPC479045 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
0.8987 High Similarity NPC176413
0.8933 High Similarity NPC479049
0.8519 High Similarity NPC294512
0.8228 Intermediate Similarity NPC479048
0.8125 Intermediate Similarity NPC479041
0.8072 Intermediate Similarity NPC483885
0.7922 Intermediate Similarity NPC70716
0.7531 Intermediate Similarity NPC6815
0.747 Intermediate Similarity NPC56953
0.7468 Intermediate Similarity NPC97667
0.7284 Intermediate Similarity NPC479042
0.7037 Intermediate Similarity NPC95265
0.6667 Remote Similarity NPC171207
0.6593 Remote Similarity NPC483868
0.6279 Remote Similarity NPC294803
0.6222 Remote Similarity NPC75600
0.6222 Remote Similarity NPC483884
0.6222 Remote Similarity NPC10904
0.6163 Remote Similarity NPC471102
0.6118 Remote Similarity NPC472569
0.6111 Remote Similarity NPC610134
0.6092 Remote Similarity NPC481064
0.6092 Remote Similarity NPC481062
0.6092 Remote Similarity NPC481058
0.6092 Remote Similarity NPC481060
0.6044 Remote Similarity NPC180668
0.6044 Remote Similarity NPC127026
0.6044 Remote Similarity NPC483890
0.593 Remote Similarity NPC57628
0.587 Remote Similarity NPC148896
0.5862 Remote Similarity NPC96903
0.5843 Remote Similarity NPC481488
0.5795 Remote Similarity NPC282239
0.5795 Remote Similarity NPC472568
0.5747 Remote Similarity NPC11685
0.5747 Remote Similarity NPC16912
0.573 Remote Similarity NPC609309
0.5699 Remote Similarity NPC483870
0.5647 Remote Similarity NPC4341
0.5579 Remote Similarity NPC483869
0.5568 Remote Similarity NPC472570
0.5556 Remote Similarity NPC481489
0.5506 Remote Similarity NPC127720
0.5465 Remote Similarity NPC479047
0.5465 Remote Similarity NPC191082
0.5465 Remote Similarity NPC291638
0.5455 Remote Similarity NPC471013
0.5444 Remote Similarity NPC147340
0.5402 Remote Similarity NPC158663
0.5349 Remote Similarity NPC483886
0.5326 Remote Similarity NPC271460
0.5294 Remote Similarity NPC6981
0.5281 Remote Similarity NPC479044
0.5281 Remote Similarity NPC41481
0.5275 Remote Similarity NPC36021
0.5243 Remote Similarity NPC483880
0.5243 Remote Similarity NPC156941
0.5227 Remote Similarity NPC139067
0.5227 Remote Similarity NPC471101
0.5172 Remote Similarity NPC17877
0.5165 Remote Similarity NPC481071
0.5165 Remote Similarity NPC184747
0.5158 Remote Similarity NPC610927
0.5104 Remote Similarity NPC301368
0.5104 Remote Similarity NPC84815
0.5056 Remote Similarity NPC67777
0.5056 Remote Similarity NPC270590
0.5056 Remote Similarity NPC27377
0.5056 Remote Similarity NPC43241
0.5053 Remote Similarity NPC481069

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC479045 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