sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2005-09-09
| Name: | Nucleoside diphosphate kinase |
|---|---|
| ID: | NDK_HALSA |
| AC: | P61136 |
| Organism: | Halobacterium salinarum |
| Reign: | Archaea |
| TaxID: | 64091 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 77 % |
| C | 3 % |
| F | 19 % |
| B-Factor: | 37.542 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.135 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.03 | 45.97 |
| According to VolSite | |
| HET Code: | CDP |
|---|---|
| Formula: | C9H12N3O11P2 |
| Molecular weight: | 400.153 g/mol |
| DrugBank ID: | DB04555 |
| Buried Surface Area: | 64.12 % |
| 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 |
|---|---|---|
| 21.4194 | -0.19212 | 20.3215 |
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 |
| C5' | CE1 | TYR- 53 | 3.93 | 0 | Hydrophobic |
| O1A | NE2 | HIS- 56 | 2.97 | 155.08 | H-Bond (Protein Donor) |
| N4 | O | GLU- 57 | 3.31 | 125.51 | H-Bond (Ligand Donor) |
| O2A | OD2 | ASP- 58 | 2.56 | 145.38 | H-Bond (Protein Donor) |
| C4' | CD1 | LEU- 65 | 3.92 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 65 | 3.69 | 0 | Hydrophobic |
| O1B | NH1 | ARG- 89 | 3.06 | 162.48 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 89 | 3.74 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 89 | 3.58 | 0 | Ionic (Protein Cationic) |
| C3' | CG2 | THR- 95 | 3.89 | 0 | Hydrophobic |
| C2' | CD1 | LEU- 113 | 3.85 | 0 | Hydrophobic |
| O2' | O | LEU- 113 | 2.82 | 165.04 | H-Bond (Ligand Donor) |
| O3' | ND2 | ASN- 116 | 2.98 | 149.15 | H-Bond (Protein Donor) |
| O1A | MG | MG- 202 | 2.32 | 0 | Metal Acceptor |
| O3B | O | HOH- 1211 | 3.26 | 179.96 | H-Bond (Protein Donor) |
