sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2011-06-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.260 | 5.270 | 5.270 | 0.010 | 5.280 | 2 |
| 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: | 31.380 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.571 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 46.94 | 53.06 |
| According to VolSite | |
| HET Code: | L8B |
|---|---|
| Formula: | C21H22N4O5 |
| Molecular weight: | 410.423 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.74 % |
| Polar Surface area: | 121.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -53.3698 | -13.27 | 2.34143 |
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 |
| CAM | CH2 | TRP- 88 | 4.07 | 0 | Hydrophobic |
| CG | CD2 | TRP- 88 | 3.66 | 0 | Hydrophobic |
| O | OH | TYR- 98 | 3.01 | 142.33 | H-Bond (Protein Donor) |
| CB | CZ | TYR- 98 | 3.55 | 0 | Hydrophobic |
| NAP | NH1 | ARG- 107 | 2.93 | 154.42 | H-Bond (Protein Donor) |
| CAY | CD1 | ILE- 109 | 4.04 | 0 | Hydrophobic |
| CAH | CG2 | ILE- 109 | 3.46 | 0 | Hydrophobic |
| NAR | O | HIS- 110 | 2.9 | 167.96 | H-Bond (Ligand Donor) |
| OD1 | OG | SER- 111 | 2.69 | 164.91 | H-Bond (Protein Donor) |
| CAA | CZ | TYR- 112 | 4.11 | 0 | Hydrophobic |
| NAQ | NE2 | HIS- 115 | 3.29 | 166.74 | H-Bond (Protein Donor) |
| OAT | NE2 | HIS- 115 | 3.4 | 156.35 | H-Bond (Protein Donor) |
| CG | CZ2 | TRP- 117 | 3.79 | 0 | Hydrophobic |
