sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2013-09-15
| Name: | Dual specificity tyrosine-phosphorylation-regulated kinase 1A |
|---|---|
| ID: | DYR1A_HUMAN |
| AC: | Q13627 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.12.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 92 % |
| D | 8 % |
| B-Factor: | 43.080 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.117 | 1073.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.34 | 55.66 |
| According to VolSite | |
| HET Code: | 2C3 |
|---|---|
| Formula: | C25H23Cl2N6O4 |
| Molecular weight: | 542.394 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.01 % |
| Polar Surface area: | 149.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -19.4712 | -6.82449 | -67.163 |
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 |
| C1 | CG2 | ILE- 165 | 3.55 | 0 | Hydrophobic |
| CL3 | CB | PHE- 170 | 3.85 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 173 | 4.38 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 173 | 3.71 | 0 | Hydrophobic |
| CL2 | CB | ALA- 186 | 3.79 | 0 | Hydrophobic |
| O25 | NZ | LYS- 188 | 2.8 | 166.08 | H-Bond (Protein Donor) |
| CL3 | CD | LYS- 188 | 3.53 | 0 | Hydrophobic |
| C32 | CD | LYS- 188 | 3.71 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 222 | 4.21 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 222 | 4.08 | 0 | Hydrophobic |
| CL2 | CB | PHE- 238 | 3.7 | 0 | Hydrophobic |
| C21 | CD2 | PHE- 238 | 3.49 | 0 | Hydrophobic |
| C21 | CB | PHE- 238 | 4 | 0 | Hydrophobic |
| O11 | N | LEU- 241 | 2.87 | 149.22 | H-Bond (Protein Donor) |
| CL2 | CD1 | LEU- 241 | 3.99 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 243 | 3.65 | 0 | Hydrophobic |
| N30 | OE1 | GLU- 291 | 3.73 | 0 | Ionic (Ligand Cationic) |
| N30 | OD1 | ASN- 292 | 2.92 | 157.94 | H-Bond (Ligand Donor) |
| C18 | CG2 | VAL- 306 | 4.25 | 0 | Hydrophobic |
| C20 | CB | VAL- 306 | 3.65 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 306 | 3.77 | 0 | Hydrophobic |
| C28 | CB | ASP- 307 | 4.12 | 0 | Hydrophobic |
| N30 | OD2 | ASP- 307 | 3.94 | 0 | Ionic (Ligand Cationic) |
