sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.240 Å
X-ray
2013-02-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.050 | 6.200 | 6.240 | 0.630 | 6.850 | 6 |
| 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: | 6.909 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.145 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 69.15 | 30.85 |
| According to VolSite | |
| HET Code: | 1K0 |
|---|---|
| Formula: | C20H22N2O5 |
| Molecular weight: | 370.399 g/mol |
| DrugBank ID: | DB12000 |
| Buried Surface Area: | 37.5 % |
| Polar Surface area: | 89.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -13.0119 | -7.2597 | 3.04919 |
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 |
| C1 | CZ3 | TRP- 81 | 3.78 | 0 | Hydrophobic |
| C1 | CB | PRO- 82 | 4.21 | 0 | Hydrophobic |
| C3 | CB | PRO- 82 | 3.71 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 83 | 3.54 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 87 | 3.7 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 87 | 3.81 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 92 | 4.02 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 92 | 3.58 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 94 | 4.39 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 94 | 3.9 | 0 | Hydrophobic |
| N1 | OD1 | ASN- 140 | 2.91 | 152.03 | H-Bond (Ligand Donor) |
| O5 | ND2 | ASN- 140 | 2.85 | 163.2 | H-Bond (Protein Donor) |
| C17 | CB | ASP- 144 | 4.13 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 146 | 4.16 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 146 | 3.74 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 146 | 4.2 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 146 | 3.66 | 0 | Hydrophobic |
