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  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC288109

*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
NPT5573 Individual Protein Beta-lactamase 1 Bacillus cereus Kcat = 0.2 /s PMID[508878]
NPT242 Individual Protein Dopamine D1 receptor Homo sapiens Potency n.a. 5804.5 nM PMID[508879]
NPT5 Individual Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Potency n.a. 37685.8 nM PMID[508879]
NPT62 Individual Protein 6-phospho-1-fructokinase Trypanosoma brucei Potency n.a. 756.9 nM PMID[508879]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 44668.4 nM PMID[508879]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 25918.5 nM PMID[508879]
NPT803 Individual Protein Flap endonuclease 1 Homo sapiens Potency n.a. 23.8 nM PMID[508879]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Ratio = 1.0 n.a. PMID[508880]
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[508880]
NPT2 Others Unspecified Potency n.a. 6309.6 nM PMID[508879]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Activity = 4.97 log10CFU PMID[508881]

☑ 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 NPC288109 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
0.8056 Intermediate Similarity NPC144780
0.7636 Intermediate Similarity NPC117829
0.6774 Remote Similarity NPC59249
0.62 Remote Similarity NPC13470
0.5865 Remote Similarity NPC103391
0.5865 Remote Similarity NPC472536
0.5846 Remote Similarity NPC298484
0.5828 Remote Similarity NPC315388
0.5821 Remote Similarity NPC473819
0.578 Remote Similarity NPC315897
0.5755 Remote Similarity NPC325750
0.5735 Remote Similarity NPC470300
0.5714 Remote Similarity NPC473495
0.5603 Remote Similarity NPC84128
0.5603 Remote Similarity NPC53858

  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 NPC288109 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
0.7982 Intermediate Similarity NPD982 Approved
0.7563 Intermediate Similarity NPD2090 Approved
0.7541 Intermediate Similarity NPD2099 Approved
0.7295 Intermediate Similarity NPD2100 Approved
0.7008 Intermediate Similarity NPD2024 Approved
0.6977 Remote Similarity NPD2025 Approved
0.6899 Remote Similarity NPD2023 Approved
0.685 Remote Similarity NPD1773 Discontinued
0.6846 Remote Similarity NPD2065 Discontinued
0.6822 Remote Similarity NPD1665 Approved
0.681 Remote Similarity NPD1784 Approved
0.6744 Remote Similarity NPD2645 Approved
0.6721 Remote Similarity NPD2147 Approved
0.6667 Remote Similarity NPD3159 Discontinued
0.66 Remote Similarity NPD2891 Approved
0.6569 Remote Similarity NPD5664 Approved
0.6569 Remote Similarity NPD4653 Approved
0.6567 Remote Similarity NPD2153 Approved
0.6544 Remote Similarity NPD4616 Suspended
0.6515 Remote Similarity NPD1806 Approved
0.6489 Remote Similarity NPD806 Approved
0.6489 Remote Similarity NPD805 Approved
0.6444 Remote Similarity NPD4088 Approved
0.6391 Remote Similarity NPD3571 Approved
0.6391 Remote Similarity NPD3572 Approved
0.6391 Remote Similarity NPD1748 Approved
0.6385 Remote Similarity NPD961 Discontinued
0.6371 Remote Similarity NPD777 Phase 3
0.637 Remote Similarity NPD3677 Clinical (unspecified phase)
0.6351 Remote Similarity NPD1979 Approved
0.6338 Remote Similarity NPD5767 Discontinued
0.6224 Remote Similarity NPD6000 Clinical (unspecified phase)
0.6216 Remote Similarity NPD1978 Approved
0.6204 Remote Similarity NPD4073 Discontinued
0.62 Remote Similarity NPD2013 Approved
0.62 Remote Similarity NPD2014 Approved
0.62 Remote Similarity NPD2016 Approved
0.6197 Remote Similarity NPD5234 Approved
0.6186 Remote Similarity NPD1749 Approved
0.6183 Remote Similarity NPD985 Approved
0.6136 Remote Similarity NPD1604 Approved
0.6136 Remote Similarity NPD1605 Approved
0.6131 Remote Similarity NPD2148 Clinical (unspecified phase)
0.6131 Remote Similarity NPD1959 Approved
0.6127 Remote Similarity NPD2419 Approved
0.6127 Remote Similarity NPD3544 Discontinued
0.6115 Remote Similarity NPD6889 Approved
0.6107 Remote Similarity NPD984 Approved
0.6102 Remote Similarity NPD4261 Phase 1
0.609 Remote Similarity NPD1263 Approved
0.6065 Remote Similarity NPD2020 Approved
0.6056 Remote Similarity NPD2418 Approved
0.6045 Remote Similarity NPD2495 Phase 3
0.6042 Remote Similarity NPD3970 Phase 3
0.6028 Remote Similarity NPD2858 Approved
0.6 Remote Similarity NPD2018 Approved
0.6 Remote Similarity NPD2019 Approved
0.5982 Remote Similarity NPD9578 Clinical (unspecified phase)
0.5974 Remote Similarity NPD6509 Phase 3
0.5957 Remote Similarity NPD2857 Approved
0.5956 Remote Similarity NPD1666 Approved
0.5956 Remote Similarity NPD1667 Approved
0.5913 Remote Similarity NPD9577 Approved
0.5903 Remote Similarity NPD4444 Discontinued
0.5903 Remote Similarity NPD3969 Clinical (unspecified phase)
0.589 Remote Similarity NPD3044 Approved
0.589 Remote Similarity NPD3045 Approved
0.5882 Remote Similarity NPD1581 Approved
0.5882 Remote Similarity NPD1782 Approved
0.5882 Remote Similarity NPD1582 Approved
0.5877 Remote Similarity NPD2683 Discontinued
0.5862 Remote Similarity NPD3285 Discontinued
0.584 Remote Similarity NPD6120 Clinical (unspecified phase)
0.5828 Remote Similarity NPD2017 Approved
0.5828 Remote Similarity NPD2890 Approved
0.5828 Remote Similarity NPD2888 Approved
0.5828 Remote Similarity NPD2889 Approved
0.5789 Remote Similarity NPD1376 Discontinued
0.578 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5769 Remote Similarity NPD3649 Discontinued
0.5743 Remote Similarity NPD2027 Approved
0.5743 Remote Similarity NPD20 Approved
0.5688 Remote Similarity NPD2262 Clinical (unspecified phase)
0.568 Remote Similarity NPD3714 Approved
0.568 Remote Similarity NPD3713 Approved
0.568 Remote Similarity NPD3715 Approved
0.5677 Remote Similarity NPD5154 Approved
0.5676 Remote Similarity NPD1676 Phase 3
0.5667 Remote Similarity NPD6077 Discontinued
0.5657 Remote Similarity NPD1986 Approved
0.5641 Remote Similarity NPD3733 Clinical (unspecified phase)
0.5635 Remote Similarity NPD4798 Approved
0.5635 Remote Similarity NPD4797 Approved
0.5633 Remote Similarity NPD4646 Approved
0.5633 Remote Similarity NPD4648 Approved
0.5633 Remote Similarity NPD4647 Approved
0.5613 Remote Similarity NPD2080 Approved
0.561 Remote Similarity NPD2251 Approved
0.561 Remote Similarity NPD2252 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