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
2006-09-05
| Name: | dCTP deaminase |
|---|---|
| ID: | DCD_ECOLI |
| AC: | P28248 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 30.938 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.432 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.34 | 53.66 |
| According to VolSite | |
| HET Code: | TTP |
|---|---|
| Formula: | C10H13N2O14P3 |
| Molecular weight: | 478.137 g/mol |
| DrugBank ID: | DB02452 |
| Buried Surface Area: | 47.15 % |
| Polar Surface area: | 279.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 17.5173 | -17.0546 | 62.3243 |
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 |
| C5M | CB | ALA- 124 | 3.99 | 0 | Hydrophobic |
| O2A | NH2 | ARG- 126 | 3.5 | 127.14 | H-Bond (Protein Donor) |
| O1G | NH2 | ARG- 126 | 3.17 | 149.13 | H-Bond (Protein Donor) |
| C2' | CG2 | ILE- 127 | 4.23 | 0 | Hydrophobic |
| O3' | N | ASP- 128 | 2.99 | 151.28 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 128 | 2.87 | 154.88 | H-Bond (Ligand Donor) |
| C2' | CD2 | TRP- 131 | 3.84 | 0 | Hydrophobic |
| C1' | CZ3 | TRP- 131 | 4.22 | 0 | Hydrophobic |
| C4' | CE3 | TRP- 131 | 4.21 | 0 | Hydrophobic |
| O2 | N | VAL- 136 | 3.18 | 130.47 | H-Bond (Protein Donor) |
| N3 | O | VAL- 136 | 2.75 | 155.89 | H-Bond (Ligand Donor) |
| C4' | CE1 | TYR- 171 | 4.09 | 0 | Hydrophobic |
| O2A | MG | MG- 195 | 2.78 | 0 | Metal Acceptor |
| O1G | MG | MG- 195 | 2.5 | 0 | Metal Acceptor |
