User Guide

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In this section, you can submit one or several molecules to get their SMILES.

  1. In this area, you can draw your molecules.
    You can also directly paste a SMILES.
    Click for more details.
  2. This button allows you to convert your molecules into SMILES.
  3. Click on Run button to calculate molecular descriptors.

You can also load SDF, mol, Txt or csv file in the second tab.

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In this section, you can observe and download the descriptors of the molecules given previously.
The molecular descriptors calculation is based on RDKIT.

  1. Download your results in an Excel or CSV file.
  2. Click on the molecule you want to zoom in: it will appear in front of the table.
  3. Find a specific value in the table.
    You can also sort the table clicking on icon.

The filters are calculated according to the following the Physical Property Subsets:


Filtering Critieria
Comments/Citation
Fragment-like LogP <=3.5 and MW <=250 and NRB <=5 Carr, Congreve, Murray and Rees, Drug Discovery Today, 2005
Lead-like MW <= 350 and MW>= 250 and LogP <= 3.5 and NRB <=7 Teague, Davis, Leeson and Oprea, Angewandte Chemie International Edition, 1999
Drug-like MW <= 500 and MW>= 150 and LogP <= 5 and NRB <=7 and TPSA < 150 and HBD <=5 and HBA <=10 Lipinski, Journal of Pharmacological and Toxicological Methods, 2000
PKI-like 1 <= NAR <= 5 and NCA <=2. No more than 2 values out of the following range : 314 <= MW <= 613, 55 <= TPSA <= 138, 3 <= HBA <= 10, HBD <= 4, 1 <= NRB <=11 and 0.7 <= ClogP <= 6.3. Carles, Bourg, Meyer and Bonnet, Molecules, 2018 ; Bournez, Carles, Peyrat, Aci-S├Ęche, Bourg, Meyer and Bonnet, Molecules, 2020
GSK 4/400 LogP < 4 and MW < 400 Gleeson, Journal of Medicinal Chemistry, 2008
Pfizer 3/75 LogP > 3 and TPSA < 75 Hughes, Blagg, Price, Bailey, DeCrescenzo, Devraj, Ellsworth, Fobian, Gibbs, Gilles, Greene, Huang, Krieger-Burke, Loesel, Wager, Whiteley, Zhang, Bioorganic & Medicinal Chemistry Letters, 2008
PAINS
Filters A, B and C were extracted from the original study of Jonathan B. Baell and Georgina A. Holloway
Baell and Holloway, Journal of Medicinal Chemistry, 2010

Greg Landrum, RDKit blogspot, 2015
HBA: Number of hydrogen bond acceptors | HBD: Number of hydrogen bond donors | LogP: Octanol-water partition coefficient | LogD: Octanol-water partition coefficient at pH=7.4 | MW: Exact molecular weight | NRB: Number of rotatable bonds | RoF: Number of rule of five (Lipinski's rule) violations | TPSA: Topological polar surface area | NHA: Number of heavy atoms | NAR: Number of aromatic cycles | NCA: Number of chiral atoms | pKa: Acid dissociation constant | FCSP3: Number of carbons with sp3 hybridization/total number of carbons | CNS MPO: Central nervous system multiparameter optimization