Ligands overview and information
Classification of Ligands
DELTA contains, for each target, information on:
- 100 Active ligands
- 100 Inactive ligands
DELTA-X contains, for each target, information on:
- N Active ligands
- N Inactive ligands
where N is defined by the minority class for each target.
Explore in Real-Time
Real-time exploration is provided only for the DELTA dataset.
All available ligands can be visulized in the Explore Ligands page. Each entry includes:
- Structure: 2D representation of the molecule
- Molecule Name: CHEMBL ID or PubChem CID
- Synonyms: Other known identifiers
- Target Name: Target on which molecule has been experimentally testes
- pChEMBL: Target-related pChEMBL value (if more than one was available the average value is reported)
Data can be filtered by Molecule Name, Synonyms, Target ID or Target Name
Please note that stereoisomers are not here reported
Information on ligands for a specific target can be visulized by clicking the link in the ‘Ligands’ column of in the Explore Targets page for the target of interest. Each entry includes:
- Structure: 2D representaion of the molecule
- Molecule Name: CHEMBL ID or PubChem CID
- SMILES: Original SMILES (before cleaning and preparation,streochemistry not included)
- Mass: Molecular weight*
- VirtualLogP: LogP of the molecule*
- pChEMBL: Target-related pChEMBL value (if more than one assay was available the average value is reported)
- Class: Active (1) or inactive (0)
Above the table, three histograms provide a visual summary of key molecular properties distribution:
- pChEMBL distribution
- Mass distribution
- LogP distribution
Data can be located by using the search bar above the table (both Molecule Name and Synonyms are supported).
Please note that stereoisomers are not here reported
Get the Full Data
Additional information on ligands dataset (for DELTA only) can be downloaded for the selected target by clicking the ‘Download Info’ button, the information includes:
- Molecule ID: DELTA unique identifier for the molecule. For stereoisomers generated from the same molecule, Molecule ID is reported as OriginatorName_StereoisomerNumber.
- Molecule Name: CHEMBL ID or PubChem CID.
- SMILES: SMILES string of the molecule. For stereoisomers, the SMILES of the generator is reported.
- N Stereoisomers: Number of stereoisomers contained in the ligand dataset.
- Class: Active (1) or inactive (0).
- pChEMBL: pChEMBL value
- The following columns report molecular descriptors calculated with VEGA ZZ and MOPAC. The table below lists all available descriptors for both VEGA ZZ and MOPAC, along with a brief explanation, for more information about descriptors please refer to VEGA ZZ manual and MOPAC manual.
Structures can be downloaded for the ligands dataset as .mol2 file by clicking the ‘Download Structures’ button
Information for the full DELTA dataset is available for download on the Explore ligands page as well as here. In the latter case, also DELTA-X data are provided.
Descriptors
Available descriptors were calculated using :
1. VEGAZZ
VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy.
| Descriptor | Info |
|---|---|
| Angles | Number of angles |
| Atoms | Number of atoms |
| Bonds | Number of bonds |
| Charge | Total charge |
| ChiralAtms | Number of chiral atoms |
| Dipole | Dipole moment (D) |
| EzBnds | Number of bonds with E/Z geometry |
| FlexTorsions | Number of flexible torsion angles |
| Gyrrad | Gyration radius (Å) |
| HbAcc | Number of hydrogen bond acceptors |
| HbDon | Number of hydrogen bond donors |
| HeavyAtoms | Number of heavy atoms |
| Impropers | Number of improper angles |
| Lipole | Lipophilicity moment |
| Mass | Molecular weight (Da) |
| Ovality | Ovality (Å) |
| Psa | Polar surface area (Ų) |
| Rings | Number of rings |
| Sas | Solvent accessible surface (Ų) |
| Sav | Solvent accessible volume (ų) |
| Sdiam | Surface diameter (Å) |
| Surface | Molecular surface (Ų) |
| Torsions | Number of torsion angles |
| Vdiam | Volume diameter (Å) |
| VirtualLogP | LogP |
| Volume | Molecular volume (ų) |
2. MOPAC
MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel’s NDDO approximation.
| Descriptor | Info |
|---|---|
| HEAT_OF_FORMATION | Enthalpy change to form a mole of compound at 25°C from its elements in their standard state (kcal/mol) |
| DIELECTRIC_ENERGY | Energy of stabilization from the interaction of charges in the solute with induced charges on the solvent-accessible surface, plus electrostatic energy due to solvent-accessible surface charge interactions. |
| DIPOLE | Dipole moment (D) |
| NO._OF_FILLED_LEVELS | Number of energy levels around the nucleus that are completely occupied with electrons |
| IONIZATION_POTENTIAL | Smallest energy required to remove an electron (eV) |
| MOLECULAR_WEIGHT | Molecular weight (Da) |
| COSMO_AREA | Continuous surface of the molecule accessible to the center of charge of a solvent molecule (Ų) |
| COSMO_VOLUME | Volume included in the COSMO surface (ų) |
| CHARGE_ON_SYSTEM | Total charge of the system |
| MULLIKEN_ELECTRONEGATIVITY | Average of the HOMO and LUMO energies, but with opposite sign (eV) |
| PARR_&_POPLE_ABSOLUTE_HARDNESS | One-half of the difference between HOMO and LUMO energy (eV) |
| SCHUURMANN_MO_SHIFT_ALPHA | Average of HOMO and LUMO energies (eV) |
| EHOMO | Energy of the Highest Occupied Molecular Orbital (eV) |
| ELUMO | Energy of the Lowest Unoccupied Molecular Orbital (eV) |
| Dn_TOTAL | Total sum of all nucleophilic delocalizabilities for each reactive center of the molecule (eV⁻¹) |
| De_TOTAL | Total sum of electrophilic delocalizabilities for each reactive center of the molecule (eV⁻¹) |
| piS_TOTAL | Self-polarizability (πS) of an atom (eV⁻¹) |