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ChEMBL-NTD

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ChEMBL-NTD User Guide

Compound Activity Search Example

1. Click on 'Compound Activity Search' link found in ChEMBL-NTD site menu.

2. You will be presented with list of available assays compounds have been tested in:



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3. (Optional) Use the slider bars to adjust minimum and maximum values for each assay:



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4. (Optional) Check 'Available Commercially ' to return compounds available in ChEMBL database.

5. Press 'Start Search' button to return compounds which match your search criteria:



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7. The results page has the following key features:

  • The results can be sorted by clicking on the appropriate column in the header bar.
  • The default results view is Mini Report Card (displayed above). This can be switched to table view, by unchecking 'Mini Report Cards' checkbox.
  • The results can be downloaded in SDF and tab-delimited text format. The tab-delimited format includes the smiles string.

8. If the search has returned no results or too many results return to the Compound Activity Search page and adjust your search criteria, (previous search criteia will be saved).

Compound Structure Search Example

1. Click on 'Compound Structure Search' link found in ChEMBL-NTD site menu.

2. You will be presented with the following search box:



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3. Click on 'Draw Compound Structure' link to open compound drawing window:



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4. When you have finished sketching the compound click 'Transfer Compound' button to transfer compound to search box:



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5. (Optional) The default compound structure search type is substructure. The search type can be changed to similarity (Tanimoto based search), using the drop down menu. If the search type is changed to similarity, the similarity cut-off value can also be changed.

6. (Optional) All compound sources are searched against by default. You can restrict the compound source to GSK, COMMERCIAL or Parent by using the drop-down menu. (Parent refers to salt-stripped set of compounds).

7. Press 'Start Search' button to return compounds which match your search criteria:



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8. The results page has the following key features:

  • The results can be sorted by clicking on the appropriate column in the header bar.
  • The default results view is Mini Report Card (displayed above). This can be switched to table view, by unchecking 'Mini Report Cards' checkbox.
  • The results can be downloaded in SDF and tab-delimited text format. The tab-delimited format includes the smiles string.

Compound Activity/Structure Search Results Column Explanations

Column Name Explanation
Compound Image of compound and link to compound report card
Sources List of compound sources and source ids, e.g. TCMDC-123462 (GSK).
If the compound is commercially available, 'COMMERCIAL' will appear in this column
Synonyms List of compound synonyms
Similarity Tanimoto similarity score between query and target structures.
This column only appears when structural similarity search is run
Mol Weight Molecular weight of compound
ALogP ALogP value for compound
PSA Polar Surface Area
HBA Hydrogen Bond Acceptors
HBD Hydrogen Bond Donors
#Ro5 Vio. Number of Rule-of-Five Violations
%IHB 3D7 (2uM) % Inhibition of P. falciparum Strain 3D7 (at 2uM)
%IHB DD2 (2uM) % Inhibition of P. falciparum DD2 (at 2uM)
%IHB 3D7 PFLDH (2uM) % Inhibition of P. falciparum strain 3D7 LDH Reporter Assay (at 2uM)
pXC50 3D7 pXC50 Determination of P. falciparum 3D7 growth
%IHB HEPG2 (10uM) % Inhibition of human HepG2 cell line (at 10uM)
IFI Inhibition Frequency Index
Annotations Compound annotations, inculding Target Hypothesis where available
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