sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.670 Å
X-ray
2013-08-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.080 | 8.080 | 8.080 | 0.000 | 8.080 | 1 |
| Name: | Tyrosine-protein kinase ITK/TSK |
|---|---|
| ID: | ITK_HUMAN |
| AC: | Q08881 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 71 % |
| B | 29 % |
| B-Factor: | 56.341 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.118 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.66 | 49.34 |
| According to VolSite | |
| HET Code: | 29Z |
|---|---|
| Formula: | C25H25N4OS |
| Molecular weight: | 429.557 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.32 % |
| Polar Surface area: | 87.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.98445 | 64.4428 | 1.95674 |
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 |
| C7 | CG2 | ILE- 369 | 3.91 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 369 | 4.16 | 0 | Hydrophobic |
| S25 | CD1 | ILE- 369 | 3.81 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 377 | 4.1 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 379 | 4.19 | 0 | Hydrophobic |
| C24 | CB | ALA- 389 | 4.22 | 0 | Hydrophobic |
| C20 | CB | ALA- 389 | 3.28 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 419 | 4.14 | 0 | Hydrophobic |
| C21 | CB | PHE- 435 | 4 | 0 | Hydrophobic |
| C13 | CZ | PHE- 437 | 3.68 | 0 | Hydrophobic |
| N16 | O | MET- 438 | 2.73 | 124.35 | H-Bond (Ligand Donor) |
| N18 | N | MET- 438 | 3.32 | 159.52 | H-Bond (Protein Donor) |
| C20 | CG | MET- 438 | 4.11 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 489 | 3.65 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 489 | 4.19 | 0 | Hydrophobic |
| C27 | CB | SER- 499 | 4.29 | 0 | Hydrophobic |
| C28 | CB | ASP- 500 | 4.46 | 0 | Hydrophobic |
| C28 | SD | MET- 503 | 4.44 | 0 | Hydrophobic |
