Natural Product: NPC608725

Natural Product IDNPC608725
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VBIRCRCPHNUJAS-LHHVKLHASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL5436765
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 VBIRCRCPHNUJAS-LHHVKLHASA-N
Standard InCHI InChI=1S/C20H20O6/c1-22-17-6-11(2-4-15(17)21)19-13-8-24-20(14(13)9-23-19)12-3-5-16-18(7-12)26-10-25-16/h2-7,13-14,19-21H,8-10H2,1H3/t13-,14-,19+,20-/m0/s1
SMILES COc1cc([C@H]2OC[C@H]3[C@@H]2CO[C@H]3c2ccc3c(c2)OCO3)ccc1O

  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
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. heartwood n.a. DOI[10.1007/s10086-012-1280-8]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[16540181]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25612070]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[31994661]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32035880]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32674448]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[34500567]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[36770639]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[37533252]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[38998569]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[39489989]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. stem n.a. Database[Article]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7870 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19310 Justicia orbiculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58038 Otoba parvifolia Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12468.1 Asarum heterotropoides var. mandshuricum Varieties Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6701 Cinnamomum camphora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19310 Justicia orbiculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7870 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6701 Cinnamomum camphora Species Lauraceae 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
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[37355024]

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 NPC608725 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 NPC88640
1.0 High Similarity NPC101153
1.0 High Similarity NPC193666
1.0 High Similarity NPC123526
0.82 Intermediate Similarity NPC27843
0.82 Intermediate Similarity NPC7171
0.8077 Intermediate Similarity NPC298317
0.8077 Intermediate Similarity NPC255566
0.7586 Intermediate Similarity NPC265154
0.75 Intermediate Similarity NPC115207
0.75 Intermediate Similarity NPC158079
0.75 Intermediate Similarity NPC228346
0.75 Intermediate Similarity NPC40432
0.75 Intermediate Similarity NPC161557
0.7407 Intermediate Similarity NPC142547
0.7407 Intermediate Similarity NPC228469
0.74 Intermediate Similarity NPC227160
0.74 Intermediate Similarity NPC82111
0.7292 Intermediate Similarity NPC171928
0.7292 Intermediate Similarity NPC158526
0.7292 Intermediate Similarity NPC129687
0.7292 Intermediate Similarity NPC33611
0.7292 Intermediate Similarity NPC16830
0.7292 Intermediate Similarity NPC100223
0.7167 Intermediate Similarity NPC487682
0.7115 Intermediate Similarity NPC189474
0.6923 Remote Similarity NPC126409
0.6923 Remote Similarity NPC99572
0.6393 Remote Similarity NPC43514
0.625 Remote Similarity NPC185071
0.6129 Remote Similarity NPC471505
0.6034 Remote Similarity NPC223185
0.6034 Remote Similarity NPC610778
0.6 Remote Similarity NPC121783
0.6 Remote Similarity NPC34902
0.6 Remote Similarity NPC18449
0.5965 Remote Similarity NPC478955
0.5965 Remote Similarity NPC478700
0.5942 Remote Similarity NPC38041
0.5942 Remote Similarity NPC22150
0.5893 Remote Similarity NPC11258
0.5893 Remote Similarity NPC21867
0.5893 Remote Similarity NPC45774
0.5893 Remote Similarity NPC74914
0.5833 Remote Similarity NPC474139
0.5833 Remote Similarity NPC483653
0.5797 Remote Similarity NPC114119
0.5797 Remote Similarity NPC471415
0.5763 Remote Similarity NPC135777
0.5763 Remote Similarity NPC469981
0.5738 Remote Similarity NPC12728
0.5714 Remote Similarity NPC67247
0.569 Remote Similarity NPC14022
0.569 Remote Similarity NPC601703
0.5672 Remote Similarity NPC470097
0.5556 Remote Similarity NPC148893
0.5556 Remote Similarity NPC222127
0.5556 Remote Similarity NPC25333
0.5556 Remote Similarity NPC49235
0.5556 Remote Similarity NPC82862
0.5536 Remote Similarity NPC469480
0.5455 Remote Similarity NPC165155
0.5455 Remote Similarity NPC24490
0.5455 Remote Similarity NPC606146
0.541 Remote Similarity NPC488984
0.541 Remote Similarity NPC488985
0.5385 Remote Similarity NPC141765
0.5385 Remote Similarity NPC34103
0.5385 Remote Similarity NPC600032
0.5352 Remote Similarity NPC51328
0.5352 Remote Similarity NPC304048
0.5352 Remote Similarity NPC55158
0.5316 Remote Similarity NPC486097
0.5303 Remote Similarity NPC64201
0.5278 Remote Similarity NPC324492
0.5278 Remote Similarity NPC317053
0.5273 Remote Similarity NPC142985
0.5263 Remote Similarity NPC147379
0.5224 Remote Similarity NPC470098
0.5224 Remote Similarity NPC473266
0.5185 Remote Similarity NPC282703
0.5185 Remote Similarity NPC184733
0.5185 Remote Similarity NPC128208
0.5185 Remote Similarity NPC129570
0.5185 Remote Similarity NPC63238
0.5185 Remote Similarity NPC602603
0.5179 Remote Similarity NPC57119
0.5179 Remote Similarity NPC158471
0.5179 Remote Similarity NPC226862
0.5167 Remote Similarity NPC274356
0.5167 Remote Similarity NPC101748
0.5156 Remote Similarity NPC477702
0.5152 Remote Similarity NPC311057
0.5088 Remote Similarity NPC312199
0.5085 Remote Similarity NPC487683
0.5085 Remote Similarity NPC479434
0.5079 Remote Similarity NPC471942
0.5077 Remote Similarity NPC488545
0.5077 Remote Similarity NPC488546
0.5075 Remote Similarity NPC487679
0.5075 Remote Similarity NPC487678
0.5072 Remote Similarity NPC281780
0.5072 Remote Similarity NPC267091
0.5065 Remote Similarity NPC486098
0.506 Remote Similarity NPC105137

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC608725 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