sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2007-11-09
| Name: | Nucleoside diphosphate kinase B |
|---|---|
| ID: | NDKB_HUMAN |
| AC: | P22392 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.4.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| C | 97 % |
| B-Factor: | 17.189 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.358 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.27 | 36.73 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 57.86 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 22.1563 | 65.2682 | 52.2797 |
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 |
| O2' | NZ | LYS- 12 | 2.91 | 130.88 | H-Bond (Protein Donor) |
| C5' | CE1 | TYR- 52 | 3.48 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 55 | 3.53 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 60 | 4.21 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 64 | 4.36 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 64 | 4.01 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 64 | 3.79 | 0 | Hydrophobic |
| O1B | CZ | ARG- 88 | 3.09 | 0 | Ionic (Protein Cationic) |
| O2B | OG1 | THR- 94 | 2.58 | 164.88 | H-Bond (Protein Donor) |
| C3' | CG2 | THR- 94 | 3.78 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 112 | 4.31 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 115 | 2.79 | 171.16 | H-Bond (Protein Donor) |
| N2 | OE1 | GLU- 152 | 3.13 | 134.56 | H-Bond (Ligand Donor) |
| O1A | MG | MG- 161 | 2.01 | 0 | Metal Acceptor |
| O3B | O | HOH- 194 | 2.69 | 179.95 | H-Bond (Protein Donor) |
| O3B | O | HOH- 198 | 2.68 | 156.99 | H-Bond (Protein Donor) |
