Natural Product: NPC124010

Natural Product IDNPC124010
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PTLYOYNZZDSYSJ-ZQDAFOGCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101505024
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003472] 2'-Hydroxychalcones

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 PTLYOYNZZDSYSJ-ZQDAFOGCSA-N
Standard InCHI InChI=1S/C25H26O4/c1-17(2)5-4-15-25(3)16-14-21-23(29-25)13-11-20(24(21)28)22(27)12-8-18-6-9-19(26)10-7-18/h5-14,16,26,28H,4,15H2,1-3H3/b12-8+/t25-/m0/s1
SMILES CC(=CCC[C@@]1(C)C=Cc2c(ccc(C(=O)/C=C/c3ccc(cc3)O)c2O)O1)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
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. root n.a. PMID[21954959]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota roots Whitessence Srl, Viterbo, Italy 2005-OCT PMID[21954959]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds LanZhou, GanSu, China early autumn (from August to the beginning of September PMID[32545196]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds DingXi, GanSu, China early autumn (from August to the beginning of September PMID[32545196]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 70 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China Maturation PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 80 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 90 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China Maturation PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 10 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 20 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 30 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 40 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 50 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 60 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 70 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 80 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 90 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 60 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 50 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 40 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 30 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 20 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 10 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14309 Desmodium tortuosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7819.1 Epichloe festucae var. lolii Varieties Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15554 Eucalyptus amplifolia Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14430 Grateloupia carnosa Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14058 Papaver pavoninum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12131 Salvia calycina Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10080 Teucrium betonicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14058 Papaver pavoninum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7819.1 Epichloe festucae var. lolii Varieties Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14430 Grateloupia carnosa Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14309 Desmodium tortuosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15554 Eucalyptus amplifolia Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10080 Teucrium betonicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12131 Salvia calycina Species Lamiaceae 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





 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 NPC124010 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 NPC483636
0.7414 Intermediate Similarity NPC156590
0.7059 Intermediate Similarity NPC488435
0.6129 Remote Similarity NPC305355
0.6087 Remote Similarity NPC488702
0.6029 Remote Similarity NPC274109
0.6 Remote Similarity NPC488700
0.5972 Remote Similarity NPC488436
0.5942 Remote Similarity NPC6118
0.5846 Remote Similarity NPC118840
0.5833 Remote Similarity NPC476981
0.5781 Remote Similarity NPC168105
0.5775 Remote Similarity NPC488701
0.5758 Remote Similarity NPC144499
0.5735 Remote Similarity NPC234255
0.5676 Remote Similarity NPC476980
0.5606 Remote Similarity NPC476006
0.5441 Remote Similarity NPC474481
0.5429 Remote Similarity NPC94155
0.5397 Remote Similarity NPC474920
0.5373 Remote Similarity NPC226636
0.5373 Remote Similarity NPC472419
0.5217 Remote Similarity NPC266689
0.5147 Remote Similarity NPC85895
0.5147 Remote Similarity NPC483639
0.5085 Remote Similarity NPC609512
0.5075 Remote Similarity NPC64908
0.5072 Remote Similarity NPC205006
0.5072 Remote Similarity NPC470087
0.507 Remote Similarity NPC484873

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC124010 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