sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.690 Å
X-ray
2009-01-27
| 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: | 43.551 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.204 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 35.45 | 64.55 |
| According to VolSite | |
| HET Code: | RUF |
|---|---|
| Formula: | C18H22ClN6O2 |
| Molecular weight: | 389.859 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.77 % |
| Polar Surface area: | 78.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 0.731222 | 5.087 | 20.8624 |
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 |
| N9 | OE1 | GLU- 205 | 3.2 | 125.4 | H-Bond (Ligand Donor) |
| N9 | OE1 | GLU- 205 | 3.2 | 0 | Ionic (Ligand Cationic) |
| N9 | OE1 | GLU- 206 | 3.17 | 156.4 | H-Bond (Ligand Donor) |
| N9 | OE1 | GLU- 206 | 3.17 | 0 | Ionic (Ligand Cationic) |
| N9 | OE2 | GLU- 206 | 3.97 | 0 | Ionic (Ligand Cationic) |
| C7 | CE1 | PHE- 357 | 4.09 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 547 | 4.44 | 0 | Hydrophobic |
| C25 | CG | TYR- 547 | 3.63 | 0 | Hydrophobic |
| C15 | CB | SER- 630 | 3.69 | 0 | Hydrophobic |
| C13 | CB | TYR- 631 | 4.14 | 0 | Hydrophobic |
| CL20 | CB | TYR- 631 | 4.29 | 0 | Hydrophobic |
| O23 | N | TYR- 631 | 3.27 | 158.5 | H-Bond (Protein Donor) |
| CL20 | CG2 | VAL- 656 | 3.82 | 0 | Hydrophobic |
| CL20 | CH2 | TRP- 659 | 4.16 | 0 | Hydrophobic |
| CL20 | CE2 | TYR- 662 | 3.83 | 0 | Hydrophobic |
| C18 | CZ | TYR- 662 | 3.47 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 666 | 4.02 | 0 | Hydrophobic |
| C11 | CD1 | TYR- 666 | 3.44 | 0 | Hydrophobic |
| C13 | CZ | TYR- 666 | 3.95 | 0 | Hydrophobic |
| CL20 | CE2 | TYR- 666 | 4.1 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 711 | 3.3 | 0 | Hydrophobic |
