sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2012-10-26
| Name: | Nucleoside diphosphate kinase |
|---|---|
| ID: | NDK_BURTA |
| AC: | Q2SWE7 |
| Organism: | Burkholderia thailandensis |
| Reign: | Bacteria |
| TaxID: | 271848 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 24.334 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.668 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.76 | 46.24 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.45 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 21.4391 | 50.6936 | -8.65122 |
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 |
| O1B | NZ | LYS- 11 | 3.27 | 161.42 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 11 | 3.5 | 131.2 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 11 | 3.27 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 11 | 3.5 | 0 | Ionic (Protein Cationic) |
| O1B | OH | TYR- 51 | 2.82 | 156.86 | H-Bond (Protein Donor) |
| C5' | CE1 | TYR- 51 | 3.53 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 59 | 3.89 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 59 | 3.63 | 0 | Aromatic Face/Face |
| C5' | CD2 | LEU- 63 | 3.94 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 63 | 3.5 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 63 | 4.36 | 0 | Hydrophobic |
| C3' | CG2 | THR- 93 | 3.88 | 0 | Hydrophobic |
| O2B | NH2 | ARG- 104 | 3.15 | 133.67 | H-Bond (Protein Donor) |
| C2' | CG1 | ILE- 111 | 3.87 | 0 | Hydrophobic |
| O2' | O | ILE- 111 | 2.7 | 164.69 | H-Bond (Ligand Donor) |
| O3' | ND2 | ASN- 114 | 2.77 | 127.53 | H-Bond (Protein Donor) |
| O2B | N | GLY- 118 | 3.49 | 161.76 | H-Bond (Protein Donor) |
