sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.590 Å
X-ray
2013-04-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.640 | 8.000 | 8.000 | 0.360 | 8.360 | 2 |
| Name: | Bromodomain-containing protein 4 |
|---|---|
| ID: | BRD4_HUMAN |
| AC: | O60885 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 7.917 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.074 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.61 | 37.39 |
| According to VolSite | |
| HET Code: | 73B |
|---|---|
| Formula: | C25H22ClN2O3 |
| Molecular weight: | 433.907 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.61 % |
| Polar Surface area: | 72.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 14.0905 | 0.71671 | 9.67739 |
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 |
| CL1 | CZ2 | TRP- 81 | 3.81 | 0 | Hydrophobic |
| C9 | CG | PRO- 82 | 4 | 0 | Hydrophobic |
| C13 | CB | PRO- 82 | 3.96 | 0 | Hydrophobic |
| C13 | CB | PRO- 82 | 3.96 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 83 | 3.89 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 87 | 4.23 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 87 | 3.98 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 87 | 4.06 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 92 | 4.16 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 92 | 4.42 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 92 | 3.87 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 92 | 3.92 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 94 | 3.81 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 97 | 4.17 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 139 | 4.1 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 140 | 3.02 | 152.03 | H-Bond (Protein Donor) |
| CL1 | CB | ASP- 145 | 4.3 | 0 | Hydrophobic |
| C7 | CB | ASP- 145 | 4.32 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 146 | 4.35 | 0 | Hydrophobic |
| C5 | CB | ILE- 146 | 4.23 | 0 | Hydrophobic |
| C18 | CG1 | ILE- 146 | 4 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 146 | 3.97 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 146 | 3.79 | 0 | Hydrophobic |
| C9 | SD | MET- 149 | 3.75 | 0 | Hydrophobic |
