sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2008-09-08
| Name: | Probable pyrophosphohydrolase |
|---|---|
| ID: | Q6MPX4_BDEBA |
| AC: | Q6MPX4 |
| Organism: | Bdellovibrio bacteriovorus |
| Reign: | Bacteria |
| TaxID: | 264462 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 56.473 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.321 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.13 | 46.88 |
| According to VolSite | |
| HET Code: | DGT |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB02181 |
| Buried Surface Area: | 51.28 % |
| Polar Surface area: | 315.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 25.0619 | -10.5442 | -14.0765 |
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' | CG1 | VAL- 24 | 4.32 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 24 | 3.66 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 24 | 4.13 | 0 | Hydrophobic |
| O2A | CZ | ARG- 40 | 3.45 | 0 | Ionic (Protein Cationic) |
| O6 | N | PHE- 52 | 3.38 | 165.6 | H-Bond (Protein Donor) |
| N1 | O | PHE- 52 | 2.87 | 142.99 | H-Bond (Ligand Donor) |
| N2 | O | PHE- 52 | 3.18 | 132.25 | H-Bond (Ligand Donor) |
| O1G | NZ | LYS- 56 | 3.28 | 121.58 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 56 | 3.1 | 154.17 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 56 | 3.28 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 56 | 3.1 | 0 | Ionic (Protein Cationic) |
| C5' | CG | LYS- 56 | 4.5 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 97 | 3.91 | 0 | Hydrophobic |
| O6 | ND2 | ASN- 136 | 2.77 | 164.5 | H-Bond (Protein Donor) |
