Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC59249

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1228 Organism Streptococcus pyogenes Streptococcus pyogenes MIC < 0.025 ug.mL-1 PMID[512976]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC < 0.025 ug.mL-1 PMID[512976]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 0.78 ug.mL-1 PMID[512976]
NPT19 Organism Escherichia coli Escherichia coli MIC = 0.1 ug.mL-1 PMID[512976]
NPT19 Organism Escherichia coli Escherichia coli MIC = 0.39 ug.mL-1 PMID[512976]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 0.2 ug.mL-1 PMID[512976]
NPT3495 Organism Morganella morganii Morganella morganii MIC = 6.25 ug.mL-1 PMID[512976]
NPT1033 Organism Enterobacter cloacae Enterobacter cloacae MIC = 0.39 ug.mL-1 PMID[512976]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 3.12 ug.mL-1 PMID[512976]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Inhibition = 0.05 % PMID[512977]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 0.04 ug.mL-1 PMID[512978]
NPT1605 Organism Enterococcus Enterococcus MIC = 5.0 ug.mL-1 PMID[512978]
NPT19 Organism Escherichia coli Escherichia coli MIC = 0.3 ug.mL-1 PMID[512978]
NPT3496 Organism Enterobacter Enterobacter MIC = 14.0 ug.mL-1 PMID[512978]
NPT3497 Organism Klebsiella sp. Klebsiella sp. MIC = 1.3 ug.mL-1 PMID[512978]
NPT2917 Organism Serratia Serratia MIC = 2.5 ug.mL-1 PMID[512978]
NPT775 Organism Proteus Proteus MIC = 7.5 ug.mL-1 PMID[512978]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 5.8 ug.mL-1 PMID[512978]
NPT26784 SINGLE PROTEIN Renal dipeptidase Homo sapiens Relative susceptibility = 1.0 n.a. PMID[512978]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 0.03 ug.mL-1 PMID[512980]
NPT1605 Organism Enterococcus Enterococcus MIC = 3.6 ug.mL-1 PMID[512980]
NPT19 Organism Escherichia coli Escherichia coli MIC = 0.37 ug.mL-1 PMID[512980]
NPT3496 Organism Enterobacter Enterobacter MIC = 0.67 ug.mL-1 PMID[512980]
NPT2916 Organism Klebsiella Klebsiella MIC = 0.88 ug.mL-1 PMID[512980]
NPT2917 Organism Serratia Serratia MIC = 0.93 ug.mL-1 PMID[512980]
NPT775 Organism Proteus Proteus MIC = 1.9 ug.mL-1 PMID[512980]
NPT2921 Organism Pseudomonas Pseudomonas MIC = 1.79 ug.mL-1 PMID[512980]
NPT26785 SINGLE PROTEIN Renal dipeptidase Sus scrofa Susceptibility = 1.0 n.a. PMID[512980]
NPT35 Others n.a. TIME = 0.5 hr PMID[512981]
NPT35 Others n.a. Stability = 80.0 % PMID[512981]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 40.0 mm PMID[512981]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 41.0 mm PMID[512981]
NPT19 Organism Escherichia coli Escherichia coli IZ = 28.5 mm PMID[512981]
NPT19 Organism Escherichia coli Escherichia coli IZ = 29.0 mm PMID[512981]
NPT1033 Organism Enterobacter cloacae Enterobacter cloacae IZ = 25.5 mm PMID[512981]
NPT1033 Organism Enterobacter cloacae Enterobacter cloacae IZ = 27.0 mm PMID[512981]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 26.0 mm PMID[512981]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC59249 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.6774 Remote Similarity NPC288109
0.6525 Remote Similarity NPC188785
0.6466 Remote Similarity NPC144780
0.6379 Remote Similarity NPC117829
0.6357 Remote Similarity NPC470788
0.6179 Remote Similarity NPC471259
0.6033 Remote Similarity NPC474985
0.6031 Remote Similarity NPC476155
0.6031 Remote Similarity NPC17581
0.6014 Remote Similarity NPC41162
0.5935 Remote Similarity NPC471258
0.5923 Remote Similarity NPC474984
0.5909 Remote Similarity NPC470300
0.5897 Remote Similarity NPC17143
0.5897 Remote Similarity NPC47230
0.5891 Remote Similarity NPC474995
0.5865 Remote Similarity NPC471261
0.5827 Remote Similarity NPC474099
0.5806 Remote Similarity NPC474244
0.5802 Remote Similarity NPC103391
0.5802 Remote Similarity NPC50694
0.5802 Remote Similarity NPC472536
0.576 Remote Similarity NPC279833
0.576 Remote Similarity NPC173690
0.576 Remote Similarity NPC80439
0.5758 Remote Similarity NPC473819
0.5726 Remote Similarity NPC474873
0.5726 Remote Similarity NPC193386
0.5725 Remote Similarity NPC309525
0.5724 Remote Similarity NPC13470
0.5714 Remote Similarity NPC64168
0.5714 Remote Similarity NPC201968
0.569 Remote Similarity NPC202056
0.5677 Remote Similarity NPC475342
0.5672 Remote Similarity NPC474006
0.5662 Remote Similarity NPC315188
0.5656 Remote Similarity NPC471257
0.5635 Remote Similarity NPC471260
0.5635 Remote Similarity NPC6271
0.5634 Remote Similarity NPC120335
0.562 Remote Similarity NPC313265
0.5615 Remote Similarity NPC469603
0.5615 Remote Similarity NPC127578
0.5606 Remote Similarity NPC469597
0.5603 Remote Similarity NPC264014
0.56 Remote Similarity NPC77703

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC59249 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9444 High Similarity NPD1773 Discontinued
0.9358 High Similarity NPD3159 Discontinued
0.9273 High Similarity NPD2645 Approved
0.9273 High Similarity NPD805 Approved
0.9273 High Similarity NPD806 Approved
0.9107 High Similarity NPD1806 Approved
0.887 High Similarity NPD3677 Clinical (unspecified phase)
0.8772 High Similarity NPD1748 Approved
0.8257 Intermediate Similarity NPD777 Phase 3
0.8235 Intermediate Similarity NPD2148 Clinical (unspecified phase)
0.7953 Intermediate Similarity NPD5767 Discontinued
0.7458 Intermediate Similarity NPD1376 Discontinued
0.7438 Intermediate Similarity NPD2495 Phase 3
0.7182 Intermediate Similarity NPD778 Phase 2
0.6929 Remote Similarity NPD1688 Phase 1
0.6891 Remote Similarity NPD3649 Discontinued
0.6829 Remote Similarity NPD2100 Approved
0.6667 Remote Similarity NPD2090 Approved
0.6667 Remote Similarity NPD2099 Approved
0.6393 Remote Similarity NPD2147 Approved
0.6325 Remote Similarity NPD1784 Approved
0.6312 Remote Similarity NPD2957 Phase 2
0.622 Remote Similarity NPD3650 Clinical (unspecified phase)
0.6121 Remote Similarity NPD161 Discontinued
0.6077 Remote Similarity NPD961 Discontinued
0.6068 Remote Similarity NPD2251 Approved
0.6068 Remote Similarity NPD2252 Approved
0.6061 Remote Similarity NPD2024 Approved
0.6036 Remote Similarity NPD5076 Approved
0.6036 Remote Similarity NPD5077 Approved
0.6015 Remote Similarity NPD1665 Approved
0.6014 Remote Similarity NPD4616 Suspended
0.5954 Remote Similarity NPD1605 Approved
0.5954 Remote Similarity NPD1604 Approved
0.5926 Remote Similarity NPD2065 Discontinued
0.5926 Remote Similarity NPD2025 Approved
0.5909 Remote Similarity NPD9578 Clinical (unspecified phase)
0.5878 Remote Similarity NPD985 Approved
0.5868 Remote Similarity NPD982 Approved
0.5865 Remote Similarity NPD4708 Discontinued
0.5852 Remote Similarity NPD3572 Approved
0.5852 Remote Similarity NPD2023 Approved
0.5852 Remote Similarity NPD3571 Approved
0.5833 Remote Similarity NPD6000 Clinical (unspecified phase)
0.5816 Remote Similarity NPD5664 Approved
0.5802 Remote Similarity NPD984 Approved
0.5797 Remote Similarity NPD4073 Discontinued
0.5764 Remote Similarity NPD3970 Phase 3
0.5734 Remote Similarity NPD4444 Discontinued
0.5724 Remote Similarity NPD2013 Approved
0.5724 Remote Similarity NPD2014 Approved
0.5724 Remote Similarity NPD2016 Approved
0.5705 Remote Similarity NPD2891 Approved
0.5704 Remote Similarity NPD4653 Approved
0.5678 Remote Similarity NPD1782 Approved
0.5674 Remote Similarity NPD7751 Phase 1
0.5672 Remote Similarity NPD1263 Approved
0.5636 Remote Similarity NPD9389 Approved
0.5612 Remote Similarity NPD1959 Approved
0.5608 Remote Similarity NPD6077 Discontinued
0.5603 Remote Similarity NPD9512 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

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