sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2012-08-31
| Name: | Von Hippel-Lindau disease tumor suppressor |
|---|---|
| ID: | VHL_HUMAN |
| AC: | P40337 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 91 % |
| L | 9 % |
| B-Factor: | 52.189 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.513 | 327.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.61 | 46.39 |
| According to VolSite | |
| HET Code: | UCK |
|---|---|
| Formula: | C19H18Cl2N2O3 |
| Molecular weight: | 393.264 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.21 % |
| Polar Surface area: | 69.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -6.11265 | 33.5632 | 1.85065 |
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 |
| C02 | CD2 | TRP- 88 | 3.84 | 0 | Hydrophobic |
| CL2 | CZ3 | TRP- 88 | 4.02 | 0 | Hydrophobic |
| C22 | CE2 | PHE- 91 | 3.49 | 0 | Hydrophobic |
| O15 | OH | TYR- 98 | 2.82 | 150.14 | H-Bond (Protein Donor) |
| C13 | CD2 | TYR- 98 | 3.49 | 0 | Hydrophobic |
| C03 | CZ | TYR- 98 | 3.98 | 0 | Hydrophobic |
| CL1 | CB | TYR- 98 | 3.97 | 0 | Hydrophobic |
| C10 | CG | PRO- 99 | 4.27 | 0 | Hydrophobic |
| CL1 | CG | PRO- 99 | 4.25 | 0 | Hydrophobic |
| CL1 | CD | ARG- 107 | 3.85 | 0 | Hydrophobic |
| C14 | CB | ILE- 109 | 3.75 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 109 | 3.6 | 0 | Hydrophobic |
| N06 | O | HIS- 110 | 2.68 | 160.22 | H-Bond (Ligand Donor) |
| O01 | OG | SER- 111 | 3.07 | 151.75 | H-Bond (Protein Donor) |
| C03 | CB | SER- 111 | 4.25 | 0 | Hydrophobic |
| O01 | ND1 | HIS- 115 | 2.6 | 147.36 | H-Bond (Protein Donor) |
| C03 | CZ2 | TRP- 117 | 3.48 | 0 | Hydrophobic |
