Natural Product: NPC607530

Natural Product IDNPC607530
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XZKJITYVVLNMNW-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3407750
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 XZKJITYVVLNMNW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C21H22O9/c1-24-12-7-10(8-13(25-2)19(12)27-4)18-21(29-6)17(23)15-11(30-18)9-14(26-3)20(28-5)16(15)22/h7-9,22H,1-6H3
SMILES COc1cc(-c2oc3cc(OC)c(OC)c(O)c3c(=O)c2OC)cc(OC)c1OC

  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
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[34964904]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[36529712]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10433 Centipeda orbicularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44688 Centipeda amplyocarpa Genus Selenomonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO60623 Cleome amplyocarpa Genus Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO63806 Cleome droserifolia Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53409 Cleome species Genus Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10433 Centipeda orbicularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2715 Murraya paniculata Species Rutaceae 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
NPT839 Cell line L6 Rattus norvegicus Activity = 99.2 % PMID[25659770]
NPT319 Cell line B16 Mus musculus IC50 = 11500.0 nM PMID[25659770]
NPT839 Cell line L6 Rattus norvegicus Activity = 53.5 % PMID[25659770]
NPT2229 Organism Trypanosoma brucei gambiense Trypanosoma brucei gambiense GI = 40.5 % PMID[25659770]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum GI = 21.7 % PMID[25659770]
NPT2229 Organism Trypanosoma brucei gambiense Trypanosoma brucei gambiense GI = 17.6 % PMID[25659770]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity > 100.0 uM PMID[25659770]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis IC50 = 21770.0 nM PMID[25659770]

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 NPC607530 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
0.8039 Intermediate Similarity NPC176300
0.7647 Intermediate Similarity NPC110070
0.7647 Intermediate Similarity NPC101830
0.75 Intermediate Similarity NPC18772
0.7407 Intermediate Similarity NPC261004
0.7321 Intermediate Similarity NPC76482
0.7308 Intermediate Similarity NPC76376
0.7255 Intermediate Similarity NPC472438
0.7222 Intermediate Similarity NPC25495
0.7037 Intermediate Similarity NPC604677
0.6923 Remote Similarity NPC75279
0.68 Remote Similarity NPC181250
0.6667 Remote Similarity NPC610359
0.6508 Remote Similarity NPC280493
0.6296 Remote Similarity NPC7973
0.614 Remote Similarity NPC29841
0.6034 Remote Similarity NPC206604
0.5926 Remote Similarity NPC602291
0.5862 Remote Similarity NPC115798
0.5862 Remote Similarity NPC69394
0.5789 Remote Similarity NPC276409
0.5763 Remote Similarity NPC235215
0.5763 Remote Similarity NPC236769
0.5763 Remote Similarity NPC7846
0.5714 Remote Similarity NPC603655
0.569 Remote Similarity NPC49824
0.5614 Remote Similarity NPC239128
0.5574 Remote Similarity NPC227192
0.5517 Remote Similarity NPC145379
0.5517 Remote Similarity NPC120163
0.55 Remote Similarity NPC93376
0.55 Remote Similarity NPC162351
0.5439 Remote Similarity NPC259058
0.5424 Remote Similarity NPC25270
0.541 Remote Similarity NPC47781
0.5345 Remote Similarity NPC203891
0.5345 Remote Similarity NPC43243
0.5345 Remote Similarity NPC266960
0.5345 Remote Similarity NPC103904
0.5345 Remote Similarity NPC262094
0.5345 Remote Similarity NPC292107
0.5312 Remote Similarity NPC99671
0.5278 Remote Similarity NPC24043
0.5278 Remote Similarity NPC27640
0.5254 Remote Similarity NPC33265
0.5254 Remote Similarity NPC105242
0.5254 Remote Similarity NPC146679
0.5254 Remote Similarity NPC188871
0.5254 Remote Similarity NPC163524
0.5254 Remote Similarity NPC143828
0.5246 Remote Similarity NPC78302
0.5246 Remote Similarity NPC58382
0.5246 Remote Similarity NPC160951
0.5246 Remote Similarity NPC18607
0.5246 Remote Similarity NPC603596
0.5172 Remote Similarity NPC250822
0.5167 Remote Similarity NPC22472
0.5167 Remote Similarity NPC9609
0.5167 Remote Similarity NPC305663
0.5161 Remote Similarity NPC19687
0.5161 Remote Similarity NPC78326
0.5161 Remote Similarity NPC284353
0.5088 Remote Similarity NPC69752
0.5082 Remote Similarity NPC300943
0.5082 Remote Similarity NPC270620
0.5082 Remote Similarity NPC246204
0.5067 Remote Similarity NPC21666

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607530 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