Natural Product: NPC607026

Natural Product IDNPC607026
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QFVOYBUQQBFCRH-VQSWZGCSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL463996
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane diterpenoids

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 QFVOYBUQQBFCRH-VQSWZGCSSA-N
Standard InCHI InChI=1S/C20H30O3/c1-13-11-19-9-5-14-17(2,7-4-8-18(14,3)16(21)22)15(19)6-10-20(13,23)12-19/h14-15,23H,1,4-12H2,2-3H3,(H,21,22)/t14-,15-,17+,18+,19+,20-/m0/s1
SMILES C=C1C[C@@]23CC[C@H]4[C@@](C)(CCC[C@@]4(C)C(=O)O)[C@@H]2CC[C@]1(O)C3

  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
NPO28194 Stevia rebaudiana Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s12010-015-1616-0]
NPO28194 Stevia rebaudiana Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.17660/ActaHortic.2008.786.31]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds n.a. PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Warminster, PA PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Onehunga, New Zealand, PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Cornell Univeristy, Ithaca PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Petone, New Zealand PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Randolph, WI PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Shenandoah, IA PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Winslow, ME PMID[17439238]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seeds Cornell University, Geneva, NY PMID[17439238]
NPO33469 Asteraceae Family Asteraceae Eukaryota n.a. n.a. n.a. PMID[18329753]
NPO28194 Stevia rebaudiana Species Asteraceae Eukaryota Leaves n.a. n.a. PMID[24758242]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Fruits Wolkowo, Poland 2016-Oct PMID[31487816]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28194 Stevia rebaudiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33469 Asteraceae Family Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44399 Bruguiera gymnorhiza L. Genus Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO441 Cucurbita maxima Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28194 Stevia rebaudiana Species Asteraceae 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
NPT3201 Individual protein Retinoic acid receptor alpha Homo sapiens Activity n.a. n.a. n.a. PMID[24799257]
NPT249 Individual protein Glucocorticoid receptor Homo sapiens Ratio = 1.45 n.a. PMID[17067160]
NPT29232 Nucleic-acid Calf thymus DNA Bos taurus Activity n.a. n.a. n.a. PMID[1812211]
NPT459 Individual protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 IC50 > 200.0 ug.mL-1 PMID[1710653]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 31622.8 nM PubChem BioAssay data set
NPT28792 Nucleic-acid Nucleic Acid n.a. Activity n.a. n.a. n.a. PMID[1812211]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT80 Cell line Raji Homo sapiens Activity > 80.0 % PMID[19131254]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 > 10000.0 nM PMID[35943432]
NPT165 Cell line HeLa Homo sapiens IC50 > 10000.0 nM PMID[35943432]
NPT83 Cell line MCF7 Homo sapiens IC50 = 185000.0 nM PMID[30059803]
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[35943432]
NPT1229 Cell line Huh-7 Homo sapiens IC50 > 10000.0 nM PMID[35943432]
NPT393 Cell line HCT-116 Homo sapiens IC50 > 10000.0 nM PMID[35943432]
NPT83 Cell line MCF7 Homo sapiens IC50 = 185000.0 nM PMID[35943432]
NPT80 Cell line Raji Homo sapiens Activity = 60.0 % PMID[19131254]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 n.a. n.a. n.a. PMID[21144747]
NPT65 Cell line HepG2 Homo sapiens IC50 n.a. n.a. n.a. PMID[21144747]
NPT3140 Cell line MGC-803 Homo sapiens IC50 n.a. n.a. n.a. PMID[21144747]
NPT1229 Cell line Huh-7 Homo sapiens TC50 = 474.5 uM PMID[27936691]
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 22.8 n.a. PMID[27936691]
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 28.6 n.a. PMID[27936691]
NPT28438 Unchecked Unchecked n.a. IC50 = 19900.0 nM PMID[27936691]
NPT28438 Unchecked Unchecked n.a. IC50 = 16600.0 nM PMID[27936691]
NPT28438 Unchecked Unchecked n.a. Activity = 91.2 % PMID[19131254]
NPT28438 Unchecked Unchecked n.a. IC50 = 340000.0 nM PMID[19131254]
NPT28438 Unchecked Unchecked n.a. Activity = 35.6 % PMID[19131254]
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 23.8 n.a. PMID[27936691]
NPT28438 Unchecked Unchecked n.a. IC50 = 20800.0 nM PMID[27936691]
NPT28438 Unchecked Unchecked n.a. IC50 > 30000.0 nM PMID[35943432]
NPT28438 Unchecked Unchecked n.a. Activity = 74.1 % PMID[19131254]
NPT28438 Unchecked Unchecked n.a. Activity = 2.1 % PMID[19131254]
NPT20 Organism Candida albicans Candida albicans MIC80 > 256.0 ug.mL-1 PMID[37787457]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Potency = 20596.2 nM PubChem BioAssay data set
NPT20 Organism Candida albicans Candida albicans MIC80 = 256.0 ug.mL-1 PMID[37787457]
NPT20 Organism Candida albicans Candida albicans MIC = 256.0 ug.mL-1 PMID[37787457]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = 27.0 % PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 87.0 % PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 3.5 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 1.8 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 67.0 % PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 93.0 % PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 3.7 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 5.4 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 4.5 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 2.3 n.a. PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 44.4 % PMID[19131254]
NPT32 Organism Mus musculus Mus musculus Activity = 60.0 % PMID[19131254]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference
Candida albicans n.a. Drug uptake n.a. n.a. n.a. PMID[37787457]





 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 NPC607026 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
0.6111 Remote Similarity NPC330659
0.6111 Remote Similarity NPC244708
0.6111 Remote Similarity NPC161187
0.5965 Remote Similarity NPC180199
0.5965 Remote Similarity NPC477919
0.5741 Remote Similarity NPC476736
0.5714 Remote Similarity NPC252032
0.5714 Remote Similarity NPC319671
0.5714 Remote Similarity NPC164210
0.5714 Remote Similarity NPC476734
0.5614 Remote Similarity NPC170985
0.5439 Remote Similarity NPC268736
0.5439 Remote Similarity NPC477931
0.5312 Remote Similarity NPC480086
0.5273 Remote Similarity NPC130459
0.5273 Remote Similarity NPC474221
0.5254 Remote Similarity NPC104806
0.5224 Remote Similarity NPC609700
0.5167 Remote Similarity NPC18819
0.5167 Remote Similarity NPC46610
0.5082 Remote Similarity NPC215893

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607026 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
0.5085 Remote Similarity NPD4224 Phase 2

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