Natural Product: NPC199459

Natural Product IDNPC199459
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (3R,5R)-3,5-Dihydroxy-1-(4-Hydroxy-3-Methoxyphenyl)-7-(4-Hydroxyphenyl)Heptane 3-O-Beta-D-Glucopyranoside
IUPAC Name (2R,3R,4S,5S,6R)-2-[(3R,5R)-5-hydroxy-1-(4-hydroxy-3-methoxyphenyl)-7-(4-hydroxyphenyl)heptan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL540446
PubChem CID 10973237
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002651] Linear diarylheptanoids
          • [CHEMONTID:0000356] Curcuminoids

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 XCZCCUNORLFCBF-DJAAXWDZSA-N
Standard InCHI InChI=1S/C26H36O10/c1-34-21-12-16(6-11-20(21)30)5-10-19(13-18(29)9-4-15-2-7-17(28)8-3-15)35-26-25(33)24(32)23(31)22(14-27)36-26/h2-3,6-8,11-12,18-19,22-33H,4-5,9-10,13-14H2,1H3/t18-,19-,22-,23-,24+,25-,26-/m1/s1
SMILES OC[C@H]1O[C@@H](O[C@@H](C[C@@H](CCc2ccc(cc2)O)O)CCc2ccc(c(c2)OC)O)[C@@H]([C@H]([C@@H]1O)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
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. root n.a. PMID[10230514]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota rhizomes SiMao City, Yunnan Province, China 1996-OCT PMID[11908966]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota Rhizomes n.a. n.a. PMID[12350150]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[12956064]
NPO12186 Oplopanax chironium Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[15104479]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. root n.a. PMID[17611928]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. leaf n.a. PMID[18649321]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[20715765]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21894904]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25608854]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[33253561]
NPO1133 Zieria laevigata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12268 Aloe littoralis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11396 Metzgeria furcata Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6266 Anzia hypoleucoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8399 Psiadia trinervia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14634 Artemisia balchanorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13527 Solanum ecuadorense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3227 Androsace umbellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10094 Daphne gnidioides Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6266 Anzia hypoleucoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12268 Aloe littoralis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14308 Coleonema pulchrum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14018 Pleurotus salmoneostramineus Species Pleurotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9487 Penicillium flexuosum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8399 Psiadia trinervia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14634 Artemisia balchanorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11753 Sideroxylon foetidissimum Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5551 Podocarpus sylvestris Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11396 Metzgeria furcata Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1133 Zieria laevigata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11909 Othonna arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9126 Stevia maimarensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11585 Geijera salicifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13723 Salvia eriophora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12186 Oplopanax chironium Species Araliaceae 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
NPT116 Cell line HL-60 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[11908966]
NPT924 Cell line HSC-2 Homo sapiens IC50 = 160.0 ug.mL-1 PMID[11908966]

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 NPC199459 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
0.9355 High Similarity NPC52277
0.8529 High Similarity NPC177035
0.8065 Intermediate Similarity NPC160854
0.8065 Intermediate Similarity NPC469704
0.8065 Intermediate Similarity NPC469703
0.7353 Intermediate Similarity NPC79715
0.7353 Intermediate Similarity NPC108659
0.6765 Remote Similarity NPC231607
0.6154 Remote Similarity NPC148055
0.6 Remote Similarity NPC17968
0.6 Remote Similarity NPC469705
0.6 Remote Similarity NPC201402
0.5692 Remote Similarity NPC473853
0.5692 Remote Similarity NPC470212
0.5571 Remote Similarity NPC215941
0.5571 Remote Similarity NPC123196
0.5571 Remote Similarity NPC311419
0.5541 Remote Similarity NPC278961
0.5541 Remote Similarity NPC113680
0.5278 Remote Similarity NPC210015
0.5278 Remote Similarity NPC65942
0.5278 Remote Similarity NPC248307
0.519 Remote Similarity NPC148273
0.5143 Remote Similarity NPC481913
0.5135 Remote Similarity NPC252307
0.5135 Remote Similarity NPC245826
0.5132 Remote Similarity NPC282409
0.5132 Remote Similarity NPC469702
0.5132 Remote Similarity NPC469661
0.5077 Remote Similarity NPC312675
0.5077 Remote Similarity NPC262156
0.5077 Remote Similarity NPC184651
0.5077 Remote Similarity NPC113865
0.507 Remote Similarity NPC602133

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC199459 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