sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2011-02-22
| Name: | Mevalonate diphosphate decarboxylase |
|---|---|
| ID: | Q9FD73_STAEP |
| AC: | Q9FD73 |
| Organism: | Staphylococcus epidermidis |
| Reign: | Bacteria |
| TaxID: | 1282 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.488 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.234 | 934.875 |
| % Hydrophobic | % Polar |
|---|---|
| 37.55 | 62.45 |
| According to VolSite | |
| HET Code: | 2P0 |
|---|---|
| Formula: | C7H9NO10P2 |
| Molecular weight: | 329.095 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.53 % |
| Polar Surface area: | 201.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -25.4764 | -20.1386 | -19.7648 |
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 |
| CB | CB | ALA- 14 | 4.16 | 0 | Hydrophobic |
| CB | CD | LYS- 17 | 3.79 | 0 | Hydrophobic |
| CB | CB | TYR- 18 | 4.44 | 0 | Hydrophobic |
| CAK | CD2 | TYR- 18 | 3.9 | 0 | Hydrophobic |
| OAF | OH | TYR- 18 | 2.73 | 158.73 | H-Bond (Protein Donor) |
| CG | CE3 | TRP- 19 | 4.17 | 0 | Hydrophobic |
| OAC | NZ | LYS- 21 | 2.56 | 169.87 | H-Bond (Protein Donor) |
| OAC | NZ | LYS- 21 | 2.56 | 0 | Ionic (Protein Cationic) |
| OAF | NZ | LYS- 21 | 3.55 | 0 | Ionic (Protein Cationic) |
| OAG | OG | SER- 139 | 3.05 | 160.87 | H-Bond (Protein Donor) |
| OAF | N | GLY- 140 | 2.87 | 152.4 | H-Bond (Protein Donor) |
| OAH | OG | SER- 141 | 2.64 | 165.53 | H-Bond (Protein Donor) |
| OAH | N | SER- 141 | 3.15 | 163.08 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 144 | 2.82 | 153.02 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 144 | 3.1 | 137.67 | H-Bond (Protein Donor) |
| O | CZ | ARG- 144 | 3.39 | 0 | Ionic (Protein Cationic) |
| OAB | OG | SER- 192 | 3.19 | 127.76 | H-Bond (Protein Donor) |
| OAM | OG | SER- 192 | 2.99 | 160.1 | H-Bond (Protein Donor) |
| CAK | CB | SER- 192 | 4.39 | 0 | Hydrophobic |
| OAC | NE | ARG- 193 | 2.75 | 170.71 | H-Bond (Protein Donor) |
| OAG | NH2 | ARG- 193 | 2.87 | 161.44 | H-Bond (Protein Donor) |
| OAC | CZ | ARG- 193 | 3.6 | 0 | Ionic (Protein Cationic) |
| OAG | CZ | ARG- 193 | 3.72 | 0 | Ionic (Protein Cationic) |
| CAK | CE | MET- 196 | 3.82 | 0 | Hydrophobic |
| CG | SD | MET- 243 | 3.83 | 0 | Hydrophobic |
| CG | CB | ASP- 283 | 4.17 | 0 | Hydrophobic |
