sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-06-03
| Name: | Nuclear pore complex protein Nup98-Nup96 |
|---|---|
| ID: | NUP98_HUMAN |
| AC: | P52948 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.037 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.179 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 29.29 | 70.71 |
| According to VolSite | |
| HET Code: | TYR_GLY_LEU |
|---|---|
| Formula: | C17H26N3O4 |
| Molecular weight: | 336.406 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.97 % |
| Polar Surface area: | 123.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 67.8965 | 103.032 | 66.5189 |
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 |
| CG | CE | LYS- 780 | 3.32 | 0 | Hydrophobic |
| CE1 | CG1 | VAL- 782 | 4.29 | 0 | Hydrophobic |
| CG | CB | VAL- 782 | 3.87 | 0 | Hydrophobic |
| CG | CG1 | VAL- 804 | 4.36 | 0 | Hydrophobic |
| CE2 | CG2 | VAL- 804 | 3.29 | 0 | Hydrophobic |
| CZ | CG2 | VAL- 804 | 3.32 | 0 | Hydrophobic |
| CB | CD1 | LEU- 806 | 4.3 | 0 | Hydrophobic |
| CD2 | CD2 | LEU- 835 | 4.2 | 0 | Hydrophobic |
| CD2 | CG2 | VAL- 838 | 3.26 | 0 | Hydrophobic |
| N | OE1 | GLN- 842 | 3.46 | 164.42 | H-Bond (Ligand Donor) |
| CD2 | CH2 | TRP- 856 | 3.96 | 0 | Hydrophobic |
| CB | CZ | PHE- 858 | 3.73 | 0 | Hydrophobic |
| CD2 | CE1 | PHE- 858 | 2.59 | 0 | Hydrophobic |
| CE2 | CG1 | VAL- 860 | 3.37 | 0 | Hydrophobic |
| CZ | CG1 | VAL- 860 | 3.24 | 0 | Hydrophobic |
| CZ | CE2 | PHE- 863 | 2.98 | 0 | Hydrophobic |
