Natural Product: NPC471909

Natural Product IDNPC471909
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (+)-Cis-(3's,4's)-Diisobutyrylkhellactone
IUPAC Name [(9S,10S)-8,8-dimethyl-9-(2-methylpropanoyloxy)-2-oxo-9,10-dihydropyrano[2,3-f]chromen-10-yl] 2-methylpropanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3290962
PubChem CID 86298516
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0003484] Pyranocoumarins
          • [CHEMONTID:0003485] Angular pyranocoumarins

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 CIVSJMYWHIZNJZ-OALUTQOASA-N
Standard InCHI InChI=1S/C22H26O7/c1-11(2)20(24)27-18-16-14(9-7-13-8-10-15(23)26-17(13)16)29-22(5,6)19(18)28-21(25)12(3)4/h7-12,18-19H,1-6H3/t18-,19-/m0/s1
SMILES CC(C)C(=O)OC1C(C(OC2=C1C3=C(C=C2)C=CC(=O)O3)(C)C)OC(=O)C(C)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
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24813739]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8874 Glehnia littoralis Species Apiaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 28200.0 nM PMID[26005918]
NPT113 Cell line RAW264.7 Mus musculus Activity > 90.0 % PMID[18494522]

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 NPC471909 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
0.9298 High Similarity NPC86892
0.8421 Intermediate Similarity NPC167111
0.8421 Intermediate Similarity NPC318400
0.8413 Intermediate Similarity NPC471625
0.8226 Intermediate Similarity NPC476455
0.8033 Intermediate Similarity NPC166672
0.7937 Intermediate Similarity NPC128529
0.7937 Intermediate Similarity NPC55615
0.7869 Intermediate Similarity NPC476457
0.7778 Intermediate Similarity NPC149320
0.7778 Intermediate Similarity NPC160727
0.7778 Intermediate Similarity NPC177281
0.75 Intermediate Similarity NPC195343
0.75 Intermediate Similarity NPC267412
0.75 Intermediate Similarity NPC471630
0.75 Intermediate Similarity NPC74655
0.75 Intermediate Similarity NPC471910
0.7385 Intermediate Similarity NPC84894
0.7385 Intermediate Similarity NPC18804
0.7385 Intermediate Similarity NPC319859
0.7385 Intermediate Similarity NPC296624
0.7385 Intermediate Similarity NPC164269
0.7385 Intermediate Similarity NPC198381
0.7385 Intermediate Similarity NPC287182
0.7385 Intermediate Similarity NPC127888
0.7101 Intermediate Similarity NPC283019
0.6957 Remote Similarity NPC100986
0.6308 Remote Similarity NPC472424
0.6308 Remote Similarity NPC281241
0.6269 Remote Similarity NPC287286
0.5781 Remote Similarity NPC199204
0.5294 Remote Similarity NPC153818
0.5294 Remote Similarity NPC232246
0.527 Remote Similarity NPC307412
0.527 Remote Similarity NPC606124
0.5211 Remote Similarity NPC469675
0.5205 Remote Similarity NPC195357
0.5205 Remote Similarity NPC152771
0.5139 Remote Similarity NPC260265
0.5135 Remote Similarity NPC312881
0.5068 Remote Similarity NPC484113

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471909 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