sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.730 Å
X-ray
2014-01-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.060 | 7.250 | 7.250 | 0.150 | 7.430 | 3 |
| 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 | 23 % |
| B | 77 % |
| B-Factor: | 15.031 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.16 | 37.84 |
| According to VolSite | |
| HET Code: | R78 |
|---|---|
| Formula: | C28H40N7O3 |
| Molecular weight: | 522.662 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 37.73 % |
| Polar Surface area: | 104.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 20.0046 | 7.98332 | 33.9226 |
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 |
| C31 | CZ3 | TRP- 81 | 4.03 | 0 | Hydrophobic |
| C16 | CZ3 | TRP- 81 | 3.5 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 87 | 3.66 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 92 | 4.08 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 92 | 4.36 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 92 | 3.58 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 94 | 4.05 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 94 | 3.61 | 0 | Hydrophobic |
| C10 | CD2 | TYR- 97 | 3.79 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 97 | 4.19 | 0 | Hydrophobic |
| C9 | CD2 | TYR- 139 | 3.81 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 140 | 2.91 | 155.31 | H-Bond (Protein Donor) |
| C5 | CG1 | ILE- 146 | 3.88 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 146 | 4.41 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 146 | 3.89 | 0 | Hydrophobic |
