sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.290 Å
X-ray
2010-06-13
| Name: | Nucleoside diphosphate kinase |
|---|---|
| ID: | Q9U1E1_LEIMA |
| AC: | Q9U1E1 |
| Organism: | Leishmania major |
| Reign: | Eukaryota |
| TaxID: | 5664 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 65.599 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.227 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 53.37 | 46.63 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.24 % |
| 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 |
|---|---|---|
| -1.80981 | -20.9255 | -46.6204 |
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 |
| O3' | NZ | LYS- 11 | 3.1 | 136.14 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 54 | 3.73 | 0 | Hydrophobic |
| C5' | CE1 | PHE- 59 | 4.1 | 0 | Hydrophobic |
| C1' | CD1 | PHE- 59 | 4.04 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 59 | 4 | 0 | Aromatic Face/Face |
| C4' | CD2 | LEU- 63 | 3.95 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 63 | 3.93 | 0 | Hydrophobic |
| O1B | CZ | ARG- 87 | 3.58 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 87 | 3.64 | 0 | Ionic (Protein Cationic) |
| O1B | NH1 | ARG- 87 | 2.76 | 143.08 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 87 | 3.45 | 126.21 | H-Bond (Protein Donor) |
| O2B | NH1 | ARG- 87 | 3.07 | 136.9 | H-Bond (Protein Donor) |
| O2B | OG1 | THR- 93 | 3.19 | 163.82 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 111 | 4.1 | 0 | Hydrophobic |
| O2' | O | VAL- 111 | 2.66 | 140.89 | H-Bond (Ligand Donor) |
| O3' | ND2 | ASN- 114 | 2.93 | 166.75 | H-Bond (Protein Donor) |
