sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2006-12-15
| Name: | Dipeptidyl peptidase 4 |
|---|---|
| ID: | DPP4_RAT |
| AC: | P14740 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.961 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.074 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 40.00 | 60.00 |
| According to VolSite | |
| HET Code: | AIL |
|---|---|
| Formula: | C13H19N4O2S2 |
| Molecular weight: | 327.446 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.15 % |
| Polar Surface area: | 132.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 12.1947 | 37.6355 | -79.6965 |
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 |
| N2 | OE2 | GLU- 203 | 2.76 | 122.06 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 203 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N2 | OE2 | GLU- 204 | 2.78 | 152.33 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 204 | 2.78 | 0 | Ionic (Ligand Cationic) |
| N2 | OE1 | GLU- 204 | 3.55 | 0 | Ionic (Ligand Cationic) |
| C11 | CB | SER- 631 | 4.2 | 0 | Hydrophobic |
| S12 | CB | TYR- 632 | 3.89 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 657 | 3.71 | 0 | Hydrophobic |
| S12 | CH2 | TRP- 660 | 4.28 | 0 | Hydrophobic |
| C11 | CZ | TYR- 663 | 4.17 | 0 | Hydrophobic |
| S12 | CE2 | TYR- 663 | 4.44 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 667 | 3.65 | 0 | Hydrophobic |
| C5 | CD1 | TYR- 667 | 3.83 | 0 | Hydrophobic |
| S12 | CE2 | TYR- 667 | 4.13 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 712 | 3.49 | 0 | Hydrophobic |
