sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2011-08-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.670 | 7.280 | 7.200 | 0.500 | 8.050 | 4 |
| 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: | 13.406 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.912 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.75 | 37.25 |
| According to VolSite | |
| HET Code: | 1GH |
|---|---|
| Formula: | C23H21N5O3 |
| Molecular weight: | 415.445 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.15 % |
| Polar Surface area: | 93.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 0.755516 | -8.1919 | 22.3693 |
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 |
| C17 | CB | PRO- 82 | 4.11 | 0 | Hydrophobic |
| C10 | CG | PRO- 82 | 3.87 | 0 | Hydrophobic |
| C4 | CB | PRO- 82 | 3.98 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 83 | 3.56 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 87 | 4.21 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 87 | 4.4 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 92 | 4.09 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 92 | 3.9 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 92 | 3.92 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 92 | 3.91 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 94 | 3.59 | 0 | Hydrophobic |
| C23 | CE1 | TYR- 97 | 4.32 | 0 | Hydrophobic |
| C21 | SG | CYS- 136 | 4.47 | 0 | Hydrophobic |
| C23 | CD2 | TYR- 139 | 3.75 | 0 | Hydrophobic |
| O3 | ND2 | ASN- 140 | 3.14 | 160.51 | H-Bond (Protein Donor) |
| C11 | CB | ASP- 145 | 4.22 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 146 | 4.26 | 0 | Hydrophobic |
| C1 | CB | ILE- 146 | 3.76 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 146 | 3.77 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 146 | 3.9 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 146 | 3.88 | 0 | Hydrophobic |
| C10 | SD | MET- 149 | 3.74 | 0 | Hydrophobic |
