Natural Product: NPC607513

Natural Product IDNPC607513
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OQKYVRDRDIXQMK-KETMJRJWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL470327
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 OQKYVRDRDIXQMK-KETMJRJWSA-N
Standard InCHI InChI=1S/C27H30O16/c28-6-15-19(33)22(36)24(38)26(41-15)18-14(42-27-25(39)23(37)20(34)16(7-29)43-27)5-13-17(21(18)35)11(32)4-12(40-13)8-1-2-9(30)10(31)3-8/h1-5,15-16,19-20,22-31,33-39H,6-7H2/t15-,16-,19-,20-,22+,23+,24-,25-,26+,27-/m1/s1
SMILES O=c1cc(-c2ccc(O)c(O)c2)oc2cc(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)c([C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)c(O)c12

  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
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. DOI[10.1111/j.1365-3040.1996.tb00393.x]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[10993146]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. Tsukuba, Japan 1998-JUN PMID[12381108]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[18270436]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23793896]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. leaf n.a. PMID[24197199]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24254087]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. seed n.a. PMID[24967651]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63152 Silene pratensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48394 Mukia maderaspatana Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9427 Lemna minor Species Araceae 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
NPT1310 Individual protein Xanthine dehydrogenase Bos taurus Inhibition = 0.0 % PMID[3379415]

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 NPC607513 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
0.7727 Intermediate Similarity NPC150767
0.7108 Intermediate Similarity NPC10807
0.7108 Intermediate Similarity NPC161881
0.6786 Remote Similarity NPC189142
0.6786 Remote Similarity NPC77660
0.6706 Remote Similarity NPC58716
0.6706 Remote Similarity NPC45638
0.6706 Remote Similarity NPC602537
0.6628 Remote Similarity NPC201292
0.6484 Remote Similarity NPC603300
0.6353 Remote Similarity NPC53545
0.6207 Remote Similarity NPC168822
0.6 Remote Similarity NPC218488
0.5909 Remote Similarity NPC39360
0.5909 Remote Similarity NPC29763
0.5909 Remote Similarity NPC210003
0.5851 Remote Similarity NPC472607
0.5843 Remote Similarity NPC93337
0.5843 Remote Similarity NPC146792
0.5833 Remote Similarity NPC3583
0.5778 Remote Similarity NPC304745
0.5778 Remote Similarity NPC105025
0.573 Remote Similarity NPC19709
0.5684 Remote Similarity NPC8856
0.5682 Remote Similarity NPC117418
0.5667 Remote Similarity NPC277205
0.5667 Remote Similarity NPC37919
0.5612 Remote Similarity NPC606373
0.5604 Remote Similarity NPC245014
0.5591 Remote Similarity NPC22832
0.5591 Remote Similarity NPC601144
0.5591 Remote Similarity NPC605067
0.5556 Remote Similarity NPC58053
0.5556 Remote Similarity NPC261866
0.5556 Remote Similarity NPC45618
0.5543 Remote Similarity NPC117260
0.5532 Remote Similarity NPC311830
0.5532 Remote Similarity NPC602805
0.5506 Remote Similarity NPC328740
0.5506 Remote Similarity NPC289774
0.5495 Remote Similarity NPC95090
0.5495 Remote Similarity NPC27408
0.5495 Remote Similarity NPC136042
0.5435 Remote Similarity NPC186807
0.5435 Remote Similarity NPC84362
0.5435 Remote Similarity NPC610763
0.5368 Remote Similarity NPC111249
0.534 Remote Similarity NPC256760
0.5326 Remote Similarity NPC259152
0.5319 Remote Similarity NPC191306
0.5319 Remote Similarity NPC488071
0.5319 Remote Similarity NPC609451
0.5312 Remote Similarity NPC190003
0.53 Remote Similarity NPC257566
0.53 Remote Similarity NPC115674
0.5263 Remote Similarity NPC243930
0.5263 Remote Similarity NPC601710
0.5253 Remote Similarity NPC78734
0.5253 Remote Similarity NPC47923
0.5217 Remote Similarity NPC83283
0.5217 Remote Similarity NPC143851
0.5208 Remote Similarity NPC605784
0.5208 Remote Similarity NPC607707
0.5204 Remote Similarity NPC254540
0.5161 Remote Similarity NPC145038
0.5161 Remote Similarity NPC282987
0.5161 Remote Similarity NPC56077
0.5161 Remote Similarity NPC281131
0.5161 Remote Similarity NPC253662
0.5161 Remote Similarity NPC179950
0.5161 Remote Similarity NPC88789
0.5161 Remote Similarity NPC491374
0.5161 Remote Similarity NPC609879
0.5135 Remote Similarity NPC132111
0.5055 Remote Similarity NPC289771
0.5053 Remote Similarity NPC42773
0.5053 Remote Similarity NPC45522
0.505 Remote Similarity NPC210073
0.5049 Remote Similarity NPC65711

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607513 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