Natural Product: NPC481060

Natural Product IDNPC481060
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AACTUSAKPIKXKW-VNYVGGQNSA-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 AACTUSAKPIKXKW-VNYVGGQNSA-N
Standard InCHI InChI=1S/C28H36O13/c1-14(29)36-13-27-19(37-15(2)30)8-10-26(7,34)28(27)22(39-17(4)32)20(25(5,6)41-28)21(38-16(3)31)23(27)40-24(33)18-9-11-35-12-18/h9,11-12,19-23,34H,8,10,13H2,1-7H3/t19-,20+,21+,22+,23-,26-,27-,28-/m0/s1
SMILES CC(=O)OC[C@]12[C@H](CC[C@@](C)([C@]32[C@@H]([C@@H]([C@H]([C@@H]1OC(=O)c1ccoc1)OC(=O)C)C(C)(C)O3)OC(=O)C)O)OC(=O)C

  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
NPO6255 Celastrus paniculatus Species Celastraceae Eukaryota n.a. root n.a. DOI[10.1016/0031-9422(90)80182-G]
NPO6255 Celastrus paniculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[32031809]
NPO6255 Celastrus paniculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6255 Celastrus paniculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6255 Celastrus paniculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6255 Celastrus paniculatus 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

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT530 Organism Caenorhabditis elegans Caenorhabditis elegans Survival = 15.29 day PMID[32031809]





 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 NPC481060 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 NPC481062
1.0 High Similarity NPC481058
0.9403 High Similarity NPC294803
0.9403 High Similarity NPC481064
0.863 High Similarity NPC180668
0.863 High Similarity NPC148896
0.8133 Intermediate Similarity NPC10904
0.7297 Intermediate Similarity NPC481063
0.7229 Intermediate Similarity NPC471013
0.7162 Intermediate Similarity NPC481059
0.7013 Intermediate Similarity NPC271460
0.6977 Remote Similarity NPC6981
0.6933 Remote Similarity NPC57628
0.6753 Remote Similarity NPC147340
0.6709 Remote Similarity NPC479049
0.6543 Remote Similarity NPC479048
0.642 Remote Similarity NPC488900
0.6296 Remote Similarity NPC6815
0.6265 Remote Similarity NPC479041
0.622 Remote Similarity NPC488899
0.6154 Remote Similarity NPC481057
0.6154 Remote Similarity NPC305403
0.6092 Remote Similarity NPC479045
0.5882 Remote Similarity NPC301368
0.5882 Remote Similarity NPC84815
0.573 Remote Similarity NPC176413
0.573 Remote Similarity NPC294512
0.5581 Remote Similarity NPC610927
0.5488 Remote Similarity NPC472569
0.5488 Remote Similarity NPC16912
0.5432 Remote Similarity NPC171207
0.5429 Remote Similarity NPC470154
0.5375 Remote Similarity NPC163719
0.5375 Remote Similarity NPC95810
0.5366 Remote Similarity NPC481061
0.5233 Remote Similarity NPC481486
0.5119 Remote Similarity NPC11685
0.5119 Remote Similarity NPC472570
0.5116 Remote Similarity NPC481489
0.5104 Remote Similarity NPC294579
0.5104 Remote Similarity NPC144779
0.5057 Remote Similarity NPC481488
0.5054 Remote Similarity NPC483885
0.5053 Remote Similarity NPC488902
0.5053 Remote Similarity NPC488903

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC481060 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