sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2007-10-05
| Name: | Dipeptidyl peptidase 4 |
|---|---|
| ID: | DPP4_HUMAN |
| AC: | P27487 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 41.244 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.013 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 32.71 | 67.29 |
| According to VolSite | |
| HET Code: | 356 |
|---|---|
| Formula: | C25H29N8O2 |
| Molecular weight: | 473.550 g/mol |
| DrugBank ID: | DB08882 |
| Buried Surface Area: | 47.46 % |
| Polar Surface area: | 115.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 67.9854 | 68.1325 | 69.9328 |
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 |
| N27 | OE2 | GLU- 205 | 2.78 | 174.65 | H-Bond (Ligand Donor) |
| N27 | OE2 | GLU- 205 | 2.78 | 0 | Ionic (Ligand Cationic) |
| N27 | OE2 | GLU- 206 | 3.06 | 0 | Ionic (Ligand Cationic) |
| N27 | OE1 | GLU- 206 | 2.57 | 0 | Ionic (Ligand Cationic) |
| N27 | OE1 | GLU- 206 | 2.57 | 155.92 | H-Bond (Ligand Donor) |
| C17 | CE1 | PHE- 357 | 3.7 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 547 | 4.41 | 0 | Hydrophobic |
| C15 | CG | TYR- 547 | 3.63 | 0 | Hydrophobic |
| C32 | CB | TRP- 629 | 4.13 | 0 | Hydrophobic |
| C35 | CE2 | TRP- 629 | 3.46 | 0 | Hydrophobic |
| C30 | CB | TRP- 629 | 3.61 | 0 | Hydrophobic |
| C31 | CB | SER- 630 | 4.46 | 0 | Hydrophobic |
| C23 | CB | SER- 630 | 4.22 | 0 | Hydrophobic |
| O10 | N | TYR- 631 | 3.21 | 143.13 | H-Bond (Protein Donor) |
| C12 | CB | TYR- 631 | 3.97 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 656 | 3.65 | 0 | Hydrophobic |
| C23 | CZ | TYR- 662 | 3.42 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 666 | 3.62 | 0 | Hydrophobic |
| C17 | CE2 | TYR- 666 | 4.18 | 0 | Hydrophobic |
| C6 | CZ | TYR- 666 | 3.58 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 711 | 3.42 | 0 | Hydrophobic |
