sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2009-01-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.700 | 8.700 | 0.000 | 8.700 | 2 |
| 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: | 44.545 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.002 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 24.44 | 75.56 |
| According to VolSite | |
| HET Code: | XIH |
|---|---|
| Formula: | C20H24N7O2 |
| Molecular weight: | 394.450 g/mol |
| DrugBank ID: | DB08743 |
| Buried Surface Area: | 56.4 % |
| Polar Surface area: | 113.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| 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 |
|---|---|---|
| 0.848897 | -12.3333 | 20.7943 |
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 |
| N14 | OE1 | GLU- 205 | 2.79 | 161.64 | H-Bond (Ligand Donor) |
| N14 | OE1 | GLU- 205 | 2.79 | 0 | Ionic (Ligand Cationic) |
| N14 | OE2 | GLU- 206 | 3.69 | 0 | Ionic (Ligand Cationic) |
| N14 | OE1 | GLU- 206 | 2.94 | 0 | Ionic (Ligand Cationic) |
| N14 | OE1 | GLU- 206 | 2.94 | 160.58 | H-Bond (Ligand Donor) |
| C10 | CE1 | PHE- 357 | 4.07 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 357 | 4.1 | 0 | Hydrophobic |
| C | CD1 | TYR- 547 | 3.59 | 0 | Hydrophobic |
| C | CB | SER- 630 | 3.92 | 0 | Hydrophobic |
| C22 | CB | SER- 630 | 3.59 | 0 | Hydrophobic |
| O | N | TYR- 631 | 3.1 | 152.16 | H-Bond (Protein Donor) |
| C19 | CB | TYR- 631 | 3.84 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 656 | 3.69 | 0 | Hydrophobic |
| C21 | CZ | TYR- 662 | 3.45 | 0 | Hydrophobic |
| C10 | CE1 | TYR- 666 | 4.27 | 0 | Hydrophobic |
| C17 | CE1 | TYR- 666 | 3.88 | 0 | Hydrophobic |
| C11 | CD1 | TYR- 666 | 4.38 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 711 | 3.55 | 0 | Hydrophobic |
| N14 | O | HOH- 906 | 2.79 | 122.33 | H-Bond (Ligand Donor) |
