sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.720 Å
X-ray
2013-01-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.440 | 6.440 | 6.440 | 0.000 | 6.440 | 1 |
| 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: | 9.824 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.908 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 65.49 | 34.51 |
| According to VolSite | |
| HET Code: | 1H2 |
|---|---|
| Formula: | C18H17NO3 |
| Molecular weight: | 295.332 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.37 % |
| Polar Surface area: | 66.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 29.0771 | 16.2886 | -1.12664 |
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 |
| O | O | PRO- 82 | 3.34 | 121.78 | H-Bond (Ligand Donor) |
| C | CB | PRO- 82 | 4.08 | 0 | Hydrophobic |
| C15 | CG | PRO- 82 | 3.8 | 0 | Hydrophobic |
| C7 | CB | PRO- 82 | 3.68 | 0 | Hydrophobic |
| C | CE1 | PHE- 83 | 3.58 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 87 | 4.18 | 0 | Hydrophobic |
| C | CG2 | VAL- 87 | 4.38 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 92 | 4.28 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 92 | 3.74 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 94 | 3.54 | 0 | Hydrophobic |
| C17 | CD2 | TYR- 139 | 4.11 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 140 | 3.09 | 168.23 | H-Bond (Protein Donor) |
| C12 | CB | ASP- 145 | 4.07 | 0 | Hydrophobic |
| C | CD1 | ILE- 146 | 3.93 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 146 | 4.02 | 0 | Hydrophobic |
| C12 | CB | ILE- 146 | 4.23 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 146 | 3.84 | 0 | Hydrophobic |
| C14 | SD | MET- 149 | 3.55 | 0 | Hydrophobic |
