sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.530 Å
X-ray
2004-10-18
| 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 |
|---|---|
| E | 37 % |
| F | 63 % |
| B-Factor: | 17.011 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.087 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.10 | 58.90 |
| According to VolSite | |
| HET Code: | DCP |
|---|---|
| Formula: | C9H12N3O13P3 |
| Molecular weight: | 463.125 g/mol |
| DrugBank ID: | DB03258 |
| Buried Surface Area: | 79.99 % |
| Polar Surface area: | 288.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| 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 |
|---|---|---|
| -16.2457 | -5.42407 | 65.3312 |
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 |
| O2B | CZ | ARG- 110 | 3.38 | 0 | Ionic (Protein Cationic) |
| O2B | NE | ARG- 110 | 2.94 | 143.27 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 110 | 2.99 | 137.58 | H-Bond (Protein Donor) |
| O2A | N | SER- 111 | 3.01 | 149.39 | H-Bond (Protein Donor) |
| O3A | N | SER- 111 | 3.34 | 141.71 | H-Bond (Protein Donor) |
| O1B | N | SER- 112 | 2.84 | 147.69 | H-Bond (Protein Donor) |
| O1B | OG | SER- 112 | 2.57 | 148.41 | H-Bond (Protein Donor) |
| N4 | O | ALA- 124 | 3.09 | 146.63 | H-Bond (Ligand Donor) |
| O1A | NH2 | ARG- 126 | 3.13 | 133.05 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 127 | 4.17 | 0 | Hydrophobic |
| C3' | CB | ASP- 128 | 4.46 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 128 | 2.73 | 167.2 | H-Bond (Ligand Donor) |
| O3' | N | ASP- 128 | 3.04 | 155.57 | H-Bond (Protein Donor) |
| C1' | CZ3 | TRP- 131 | 3.72 | 0 | Hydrophobic |
| C4' | CZ3 | TRP- 131 | 3.89 | 0 | Hydrophobic |
| C2' | CE3 | TRP- 131 | 3.74 | 0 | Hydrophobic |
| O2 | N | VAL- 136 | 3.01 | 154.72 | H-Bond (Protein Donor) |
| N4 | O | VAL- 136 | 3.19 | 133.44 | H-Bond (Ligand Donor) |
| C4' | CZ | TYR- 171 | 4 | 0 | Hydrophobic |
| C5' | CE1 | TYR- 171 | 3.98 | 0 | Hydrophobic |
| O2G | OH | TYR- 171 | 2.56 | 139.94 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 174 | 3.33 | 146.26 | H-Bond (Protein Donor) |
| O3G | NH1 | ARG- 174 | 3.29 | 148.78 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 174 | 3.76 | 0 | Ionic (Protein Cationic) |
| O1G | NZ | LYS- 178 | 3.27 | 0 | Ionic (Protein Cationic) |
| O2G | N | LYS- 178 | 2.83 | 156.66 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 182 | 2.73 | 147.66 | H-Bond (Protein Donor) |
| O1A | MG | MG- 5195 | 1.91 | 0 | Metal Acceptor |
| O2B | MG | MG- 5195 | 2.15 | 0 | Metal Acceptor |
| O3G | MG | MG- 5195 | 2.04 | 0 | Metal Acceptor |
