Natural Product: NPC610927

Natural Product IDNPC610927
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NZDZSXKCSHEVTK-KMASGLHRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2272201
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 NZDZSXKCSHEVTK-KMASGLHRSA-N
Standard InCHI InChI=1S/C32H37NO10/c1-18(34)39-24-23-25(42-28(37)21-13-10-16-33-17-21)32(43-29(23,3)4)30(5,38)15-14-22(31(32,6)26(24)40-19(2)35)41-27(36)20-11-8-7-9-12-20/h7-13,16-17,22-26,38H,14-15H2,1-6H3/t22-,23+,24-,25+,26+,30-,31-,32-/m0/s1
SMILES CC(=O)O[C@H]1[C@@H]2[C@@H](OC(=O)c3cccnc3)[C@@]3(OC2(C)C)[C@@](C)([C@@H](OC(=O)c2ccccc2)CC[C@]3(C)O)[C@@H]1OC(C)=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
NPO10656 Rzedowskia tolantonguensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10656 Rzedowskia tolantonguensis 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
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.45 n.a. DOI[10.1016/S0305-1978(97)00035-5]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 100.0 % DOI[10.1016/0305-1978(92)90042-C]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.15 n.a. DOI[10.1016/0305-1978(92)90042-C]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.04 n.a. DOI[10.1016/0305-1978(92)90042-C]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.45 n.a. DOI[10.1016/0305-1978(92)90042-C]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.04 n.a. DOI[10.1016/S0305-1978(97)00035-5]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis FR50 = 0.15 n.a. DOI[10.1016/S0305-1978(97)00035-5]

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 NPC610927 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
0.9041 High Similarity NPC301368
0.9041 High Similarity NPC84815
0.7468 Intermediate Similarity NPC611111
0.7397 Intermediate Similarity NPC163719
0.7397 Intermediate Similarity NPC95810
0.7368 Intermediate Similarity NPC127720
0.7 Intermediate Similarity NPC212768
0.6706 Remote Similarity NPC253738
0.6667 Remote Similarity NPC148896
0.6585 Remote Similarity NPC4421
0.6386 Remote Similarity NPC608007
0.6353 Remote Similarity NPC56953
0.6333 Remote Similarity NPC471013
0.6279 Remote Similarity NPC127026
0.6279 Remote Similarity NPC483890
0.618 Remote Similarity NPC483885
0.6173 Remote Similarity NPC57628
0.6129 Remote Similarity NPC6981
0.6092 Remote Similarity NPC10904
0.6076 Remote Similarity NPC200471
0.6076 Remote Similarity NPC472575
0.6071 Remote Similarity NPC483887
0.6071 Remote Similarity NPC158020
0.5914 Remote Similarity NPC471980
0.5909 Remote Similarity NPC180668
0.5889 Remote Similarity NPC30171
0.5862 Remote Similarity NPC125106
0.5862 Remote Similarity NPC472573
0.5802 Remote Similarity NPC472572
0.5765 Remote Similarity NPC294803
0.575 Remote Similarity NPC483886
0.5595 Remote Similarity NPC472570
0.5581 Remote Similarity NPC481062
0.5581 Remote Similarity NPC481058
0.5581 Remote Similarity NPC481060
0.5568 Remote Similarity NPC483889
0.5556 Remote Similarity NPC483870
0.5484 Remote Similarity NPC176413
0.5484 Remote Similarity NPC294512
0.5408 Remote Similarity NPC483880
0.5408 Remote Similarity NPC156941
0.5402 Remote Similarity NPC609309
0.5385 Remote Similarity NPC473115
0.5385 Remote Similarity NPC75600
0.5385 Remote Similarity NPC483884
0.5366 Remote Similarity NPC281717
0.5349 Remote Similarity NPC481063
0.5342 Remote Similarity NPC470154
0.5333 Remote Similarity NPC483881
0.5301 Remote Similarity NPC291599
0.5233 Remote Similarity NPC472569
0.5233 Remote Similarity NPC16912
0.5227 Remote Similarity NPC481064
0.5185 Remote Similarity NPC476094
0.5169 Remote Similarity NPC483875
0.5158 Remote Similarity NPC479045
0.5059 Remote Similarity NPC270590
0.5056 Remote Similarity NPC481489
0.5055 Remote Similarity NPC488900
0.5055 Remote Similarity NPC488899
0.5051 Remote Similarity NPC294579
0.5051 Remote Similarity NPC144779

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC610927 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