sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2010-05-14
| Name: | Dipeptidyl peptidase 2 |
|---|---|
| ID: | DPP2_HUMAN |
| AC: | Q9UHL4 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.14.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 40.471 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.404 | 1012.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.67 | 51.33 |
| According to VolSite | |
| HET Code: | OPY |
|---|---|
| Formula: | C9H21N3O |
| Molecular weight: | 187.283 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.82 % |
| Polar Surface area: | 75.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 1.72346 | 18.7242 | 63.1025 |
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 |
| NAA | OE2 | GLU- 78 | 2.8 | 174.46 | H-Bond (Ligand Donor) |
| NAA | OE2 | GLU- 78 | 2.8 | 0 | Ionic (Ligand Cationic) |
| CAF | CB | SER- 162 | 4.32 | 0 | Hydrophobic |
| CAE | CB | TYR- 163 | 4.21 | 0 | Hydrophobic |
| CAE | SD | MET- 166 | 4.4 | 0 | Hydrophobic |
| CAF | CG | PRO- 188 | 3.46 | 0 | Hydrophobic |
| N | OD2 | ASP- 334 | 3.31 | 0 | Ionic (Ligand Cationic) |
| N | OG1 | THR- 336 | 2.77 | 161.3 | H-Bond (Ligand Donor) |
| N | O | GLY- 337 | 2.65 | 165.45 | H-Bond (Ligand Donor) |
| CB | CE2 | TRP- 347 | 3.93 | 0 | Hydrophobic |
| CAG | CZ2 | TRP- 347 | 3.82 | 0 | Hydrophobic |
| CAG | CD2 | LEU- 357 | 4.23 | 0 | Hydrophobic |
| O | NE1 | TRP- 420 | 3.21 | 126.02 | H-Bond (Protein Donor) |
| CAF | CE2 | TRP- 420 | 3.61 | 0 | Hydrophobic |
| CAG | CH2 | TRP- 420 | 4.31 | 0 | Hydrophobic |
