sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-10-19
| Name: | 2,2-dialkylglycine decarboxylase |
|---|---|
| ID: | DGDA_BURCE |
| AC: | P16932 |
| Organism: | Burkholderia cepacia |
| Reign: | Bacteria |
| TaxID: | 292 |
| EC Number: | 4.1.1.64 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.147 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.259 | 310.500 |
| % Hydrophobic | % Polar |
|---|---|
| 39.13 | 60.87 |
| According to VolSite | |
| HET Code: | 5PA |
|---|---|
| Formula: | C12H15N2O7P |
| Molecular weight: | 330.230 g/mol |
| DrugBank ID: | DB02849 |
| Buried Surface Area: | 58.07 % |
| Polar Surface area: | 172.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 17.3816 | 51.462 | 17.3475 |
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 |
| O7 | NE2 | GLN- 52 | 3.3 | 136.91 | H-Bond (Protein Donor) |
| C9 | CG | GLN- 52 | 4.1 | 0 | Hydrophobic |
| O2P | N | GLY- 111 | 3.49 | 152.87 | H-Bond (Protein Donor) |
| O3P | N | ALA- 112 | 2.92 | 164.04 | H-Bond (Protein Donor) |
| C8 | CE2 | TRP- 138 | 4.01 | 0 | Hydrophobic |
| C10 | CZ2 | TRP- 138 | 3.8 | 0 | Hydrophobic |
| C2A | CG | GLU- 210 | 3.69 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 243 | 2.78 | 159.6 | H-Bond (Protein Donor) |
| C2A | CB | ALA- 245 | 3.84 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 246 | 3.16 | 133.68 | H-Bond (Protein Donor) |
| O7 | NZ | LYS- 272 | 3.19 | 140.64 | H-Bond (Protein Donor) |
| O7 | NZ | LYS- 272 | 3.19 | 0 | Ionic (Protein Cationic) |
| O7 | NH2 | ARG- 406 | 3.02 | 166.75 | H-Bond (Protein Donor) |
| O8 | NH2 | ARG- 406 | 3.23 | 128.25 | H-Bond (Protein Donor) |
| O7 | CZ | ARG- 406 | 3.72 | 0 | Ionic (Protein Cationic) |
| O8 | CZ | ARG- 406 | 3.93 | 0 | Ionic (Protein Cationic) |
