sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-02-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.300 | 6.390 | 6.160 | 1.010 | 8.140 | 5 |
| Name: | D-amino-acid oxidase |
|---|---|
| ID: | OXDA_HUMAN |
| AC: | P14920 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.4.3.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 53.630 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.292 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 66.96 | 33.04 |
| According to VolSite | |
| HET Code: | SE5 |
|---|---|
| Formula: | C13H11ClNO2 |
| Molecular weight: | 248.685 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.93 % |
| Polar Surface area: | 55.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.31376 | -7.31988 | -19.7235 |
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 |
| C5 | CD2 | LEU- 51 | 3.76 | 0 | Hydrophobic |
| C8 | CB | GLN- 53 | 3.86 | 0 | Hydrophobic |
| C13 | CG | GLN- 53 | 4.24 | 0 | Hydrophobic |
| CL1 | CB | LEU- 56 | 4.36 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 215 | 3.72 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 215 | 4 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 223 | 3.26 | 0 | Hydrophobic |
| CL1 | CE1 | TYR- 224 | 4.19 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 230 | 3.82 | 0 | Hydrophobic |
| O1 | CZ | ARG- 283 | 3.87 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 283 | 3.37 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 283 | 3.11 | 173.29 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 283 | 3.41 | 122.51 | H-Bond (Protein Donor) |
| N1 | O | GLY- 313 | 2.56 | 136.15 | H-Bond (Ligand Donor) |
