sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2010-07-12
| Name: | Cytidylate kinase |
|---|---|
| ID: | KCY_THET8 |
| AC: | Q5SL35 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.830 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.373 | 1086.750 |
| % Hydrophobic | % Polar |
|---|---|
| 34.47 | 65.53 |
| According to VolSite | |
| HET Code: | CDP |
|---|---|
| Formula: | C9H12N3O11P2 |
| Molecular weight: | 400.153 g/mol |
| DrugBank ID: | DB04555 |
| Buried Surface Area: | 65.29 % |
| Polar Surface area: | 249.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 33.5492 | 25.1192 | 4.37888 |
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 |
| O3B | N | ALA- 12 | 3.23 | 155.94 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 15 | 3.04 | 157.67 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 15 | 2.79 | 121.46 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 15 | 3.04 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 15 | 2.79 | 0 | Ionic (Protein Cationic) |
| N4 | OG | SER- 33 | 3.12 | 140.68 | H-Bond (Ligand Donor) |
| C4' | CB | TYR- 37 | 4.42 | 0 | Hydrophobic |
| C1' | CB | TYR- 37 | 3.88 | 0 | Hydrophobic |
| O3A | NH2 | ARG- 38 | 3.21 | 168.51 | H-Bond (Protein Donor) |
| O2A | NE | ARG- 38 | 2.9 | 157.14 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 38 | 3.91 | 0 | Ionic (Protein Cationic) |
| C5' | CG | ARG- 38 | 4.1 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 97 | 4.37 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 97 | 3.78 | 0 | Hydrophobic |
| C3' | CG1 | VAL- 97 | 4.46 | 0 | Hydrophobic |
| C1' | CB | ALA- 101 | 3.81 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 107 | 2.84 | 174.8 | H-Bond (Protein Donor) |
| N3 | NH2 | ARG- 107 | 3 | 157.41 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 126 | 3.1 | 171.26 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 126 | 3.01 | 125.02 | H-Bond (Protein Donor) |
| O2B | CZ | ARG- 126 | 3.1 | 0 | Ionic (Protein Cationic) |
| N4 | OD1 | ASP- 127 | 2.97 | 163.06 | H-Bond (Ligand Donor) |
| O1A | O | HOH- 215 | 2.68 | 167.79 | H-Bond (Protein Donor) |
| O1A | O | HOH- 297 | 2.7 | 166.31 | H-Bond (Protein Donor) |
