sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-10-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.960 | 4.960 | 4.960 | 0.000 | 4.960 | 1 |
| Name: | Thymidylate kinase |
|---|---|
| ID: | Q8I4S1_PLAF7 |
| AC: | Q8I4S1 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 18.950 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.055 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.27 | 54.73 |
| According to VolSite | |
| HET Code: | WMJ |
|---|---|
| Formula: | C17H19N5O7 |
| Molecular weight: | 405.362 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.05 % |
| Polar Surface area: | 165.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 12.6889 | 8.21838 | 32.9339 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| CAA | CB | PHE- 44 | 3.86 | 0 | Hydrophobic |
| CAN | CD2 | LEU- 59 | 3.61 | 0 | Hydrophobic |
| CAJ | CB | LEU- 59 | 4.13 | 0 | Hydrophobic |
| CAA | CD1 | PHE- 74 | 4.14 | 0 | Hydrophobic |
| CAN | CZ | PHE- 74 | 4 | 0 | Hydrophobic |
| OAC | NH2 | ARG- 78 | 3.45 | 129.77 | H-Bond (Protein Donor) |
| OAC | NH1 | ARG- 78 | 2.81 | 160.3 | H-Bond (Protein Donor) |
| CAA | CB | ARG- 99 | 3.96 | 0 | Hydrophobic |
| CAZ | CD | ARG- 99 | 3.94 | 0 | Hydrophobic |
| CAA | CB | SER- 103 | 3.88 | 0 | Hydrophobic |
| CBA | CD2 | TYR- 107 | 3.59 | 0 | Hydrophobic |
| CAN | CE2 | TYR- 153 | 4.03 | 0 | Hydrophobic |
