sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
1999-04-06
| Name: | Pyridoxamine 5'-phosphate oxidase |
|---|---|
| ID: | PDX3_YEAST |
| AC: | P38075 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.4.3.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 37 % |
| B | 63 % |
| B-Factor: | 31.013 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.888 | 1161.000 |
| % Hydrophobic | % Polar |
|---|---|
| 38.66 | 61.34 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 69.35 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -40.4844 | 4.956 | 0.620097 |
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 |
| C7M | CD2 | LEU- 54 | 4.34 | 0 | Hydrophobic |
| C2' | CG | ARG- 73 | 3.94 | 0 | Hydrophobic |
| C3' | CB | ARG- 73 | 4.04 | 0 | Hydrophobic |
| C4' | CG | ARG- 73 | 3.57 | 0 | Hydrophobic |
| C5' | CD | ARG- 73 | 4.15 | 0 | Hydrophobic |
| O1P | CZ | ARG- 73 | 3.55 | 0 | Ionic (Protein Cationic) |
| O1P | NH1 | ARG- 73 | 2.66 | 147.27 | H-Bond (Protein Donor) |
| C8 | CG2 | ILE- 74 | 3.82 | 0 | Hydrophobic |
| C8M | CB | ILE- 74 | 3.94 | 0 | Hydrophobic |
| C9 | CB | ILE- 74 | 4.22 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 74 | 3.71 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 75 | 3.78 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 76 | 3.99 | 0 | Hydrophobic |
| O5' | NZ | LYS- 96 | 2.66 | 123.96 | H-Bond (Protein Donor) |
| O3P | N | LYS- 96 | 2.61 | 173.68 | H-Bond (Protein Donor) |
| O3P | NZ | LYS- 96 | 3.74 | 0 | Ionic (Protein Cationic) |
| C7M | CZ | PHE- 111 | 3.44 | 0 | Hydrophobic |
| C8M | CE2 | PHE- 111 | 3.51 | 0 | Hydrophobic |
| C8M | CB | GLN- 118 | 4.44 | 0 | Hydrophobic |
| O2' | NE2 | GLN- 118 | 3.24 | 165.55 | H-Bond (Protein Donor) |
| O1P | NH1 | ARG- 120 | 2.94 | 133.46 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 120 | 3.31 | 124.01 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 120 | 3.49 | 0 | Ionic (Protein Cationic) |
| O2 | NE2 | GLN- 153 | 3.1 | 160.37 | H-Bond (Protein Donor) |
| C5' | CG | GLN- 153 | 4.26 | 0 | Hydrophobic |
| C8M | CH2 | TRP- 199 | 3.34 | 0 | Hydrophobic |
| O2P | CZ | ARG- 209 | 3.55 | 0 | Ionic (Protein Cationic) |
| O2P | NH2 | ARG- 209 | 2.91 | 147.9 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 209 | 3.35 | 130.95 | H-Bond (Protein Donor) |
