sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-03-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.280 | 7.540 | 7.620 | 0.190 | 7.720 | 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 | 100 % |
| B-Factor: | 25.872 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.215 | 391.500 |
| % Hydrophobic | % Polar |
|---|---|
| 56.03 | 43.97 |
| According to VolSite | |
| HET Code: | WSH |
|---|---|
| Formula: | C25H21N5O2 |
| Molecular weight: | 423.467 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.23 % |
| Polar Surface area: | 81.4 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: | 5 |
| X | Y | Z |
|---|---|---|
| -5.34313 | -7.08825 | -18.3212 |
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 | CB | PRO- 375 | 4.43 | 0 | Hydrophobic |
| C15 | CG | PRO- 375 | 3.92 | 0 | Hydrophobic |
| C23 | CB | PRO- 375 | 4.21 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 376 | 3.93 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 380 | 4.2 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 380 | 4 | 0 | Hydrophobic |
| C12 | CG | LEU- 385 | 4.31 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 385 | 3.82 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 387 | 3.72 | 0 | Hydrophobic |
| N2 | ND2 | ASN- 433 | 2.95 | 169.56 | H-Bond (Protein Donor) |
| N1 | ND2 | ASN- 433 | 3.49 | 148.21 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 433 | 3.12 | 138.65 | H-Bond (Ligand Donor) |
| C17 | CB | GLU- 438 | 4.14 | 0 | Hydrophobic |
| C16 | CB | VAL- 439 | 4.28 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 439 | 3.55 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 439 | 4.14 | 0 | Hydrophobic |
| C14 | CB | VAL- 439 | 3.68 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 439 | 4.15 | 0 | Hydrophobic |
| C16 | SD | MET- 442 | 3.85 | 0 | Hydrophobic |
