sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2014-06-03
| Name: | Nucleoside diphosphate kinase |
|---|---|
| ID: | A5J299_LITVA |
| AC: | A5J299 |
| Organism: | Litopenaeus vannamei |
| Reign: | Eukaryota |
| TaxID: | 6689 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 5 % |
| C | 95 % |
| B-Factor: | 20.831 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.167 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.86 | 44.14 |
| According to VolSite | |
| HET Code: | DAT |
|---|---|
| Formula: | C10H12N5O9P2 |
| Molecular weight: | 408.178 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.57 % |
| Polar Surface area: | 240.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -22.7249 | -37.404 | 7.03673 |
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- 51 | 3.44 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 54 | 3.74 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 59 | 4.05 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 59 | 3.84 | 0 | Aromatic Face/Face |
| C1' | CD1 | LEU- 63 | 3.99 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 63 | 3.92 | 0 | Hydrophobic |
| O3B | NH1 | ARG- 87 | 2.93 | 170.82 | H-Bond (Protein Donor) |
| O3B | CZ | ARG- 87 | 3.78 | 0 | Ionic (Protein Cationic) |
| O1B | OG1 | THR- 93 | 2.55 | 170.95 | H-Bond (Protein Donor) |
| C3' | CG2 | THR- 93 | 4.1 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 111 | 4.35 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 114 | 2.98 | 173.72 | H-Bond (Protein Donor) |
| O3B | MG | MG- 1153 | 2.62 | 0 | Metal Acceptor |
| O1A | MG | MG- 1153 | 2.62 | 0 | Metal Acceptor |
| O2B | O | HOH- 2015 | 3.03 | 179.97 | H-Bond (Protein Donor) |
| O2B | O | HOH- 2069 | 2.68 | 171.54 | H-Bond (Protein Donor) |
