Natural Product: NPC601565

Natural Product IDNPC601565
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SQGLUEWZRKIEGS-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL374055
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 SQGLUEWZRKIEGS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C32H22O10/c1-39-18-6-3-15(4-7-18)25-13-23(37)31-24(38)14-27(40-2)29(32(31)42-25)19-9-16(5-8-20(19)34)26-12-22(36)30-21(35)10-17(33)11-28(30)41-26/h3-14,33-35,38H,1-2H3
SMILES COc1ccc(-c2cc(=O)c3c(O)cc(OC)c(-c4cc(-c5cc(=O)c6c(O)cc(O)cc6o5)ccc4O)c3o2)cc1

  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
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[17869103]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. stem n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[21226514]
NPO20082 Podocarpus latifolius Species Podocarpaceae Eukaryota n.a. root n.a. PMID[21306129]
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[26905523]
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20082 Podocarpus latifolius Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44134 Ouratea multiflora Species Ochnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO64202 Lagarostrobos spp. Genus Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO46381 Dacrydium spp. Genus Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14722 Callitris columellaris Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14722 Callitris columellaris Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19278 Taxodium distichum Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20082 Podocarpus latifolius Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae 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
NPT740 Individual protein Beta-secretase 1 Homo sapiens IC50 > 10000.0 nM PMID[20598535]
NPT30107 Single protein Amyloid-beta A4 protein Homo sapiens IC50 = 20100.0 nM PMID[31138471]
NPT3595 Individual protein Cathepsin K Homo sapiens IC50 = 0.89 ug.mL-1 PMID[17027271]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT139 Cell line HT-29 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT90 Cell line DU-145 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT81 Cell line A549 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT319 Cell line B16 Mus musculus IC50 = 1.6 ug.mL-1 PMID[17027271]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 55.3 % PMID[26004578]

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 NPC601565 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
0.8955 High Similarity NPC290830
0.8143 Intermediate Similarity NPC303485
0.8143 Intermediate Similarity NPC158027
0.8028 Intermediate Similarity NPC186227
0.7671 Intermediate Similarity NPC215203
0.75 Intermediate Similarity NPC603508
0.72 Intermediate Similarity NPC121649
0.7077 Intermediate Similarity NPC231772
0.7027 Intermediate Similarity NPC150908
0.6912 Remote Similarity NPC610914
0.6711 Remote Similarity NPC71061
0.6667 Remote Similarity NPC52611
0.6623 Remote Similarity NPC194593
0.6528 Remote Similarity NPC138299
0.6447 Remote Similarity NPC248739
0.641 Remote Similarity NPC159707
0.6364 Remote Similarity NPC600972
0.6364 Remote Similarity NPC601984
0.6301 Remote Similarity NPC111112
0.6282 Remote Similarity NPC72425
0.6203 Remote Similarity NPC14606
0.6173 Remote Similarity NPC265624
0.6056 Remote Similarity NPC12200
0.5972 Remote Similarity NPC183950
0.5897 Remote Similarity NPC259757
0.5833 Remote Similarity NPC52005
0.5789 Remote Similarity NPC291746
0.5714 Remote Similarity NPC29353
0.5672 Remote Similarity NPC50898
0.5663 Remote Similarity NPC18699
0.5663 Remote Similarity NPC205026
0.5647 Remote Similarity NPC55443
0.5641 Remote Similarity NPC183
0.5634 Remote Similarity NPC483773
0.557 Remote Similarity NPC610480
0.5422 Remote Similarity NPC272064
0.5417 Remote Similarity NPC62536
0.5417 Remote Similarity NPC234133
0.5417 Remote Similarity NPC120464
0.5417 Remote Similarity NPC601901
0.5395 Remote Similarity NPC605634
0.5385 Remote Similarity NPC112954
0.5375 Remote Similarity NPC603692
0.5286 Remote Similarity NPC279121
0.5278 Remote Similarity NPC156222
0.525 Remote Similarity NPC196179
0.525 Remote Similarity NPC254351
0.5217 Remote Similarity NPC78540
0.5205 Remote Similarity NPC184136
0.5205 Remote Similarity NPC59951
0.5205 Remote Similarity NPC241838
0.5205 Remote Similarity NPC266597
0.52 Remote Similarity NPC606638
0.519 Remote Similarity NPC288840
0.5176 Remote Similarity NPC143851
0.5135 Remote Similarity NPC603662
0.5068 Remote Similarity NPC600177
0.5065 Remote Similarity NPC67322
0.5062 Remote Similarity NPC34089

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC601565 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
0.5286 Remote Similarity NPD1511 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