sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2015-06-02
| Name: | Bromodomain-containing protein 2 |
|---|---|
| ID: | BRD2_HUMAN |
| AC: | P25440 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 9.377 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.217 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.69 | 43.31 |
| According to VolSite | |
| HET Code: | 2LO |
|---|---|
| Formula: | C28H34ClN4O3 |
| Molecular weight: | 510.048 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 37.68 % |
| Polar Surface area: | 66.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -20.1485 | -2.59719 | -8.64339 |
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 |
| C10 | CZ3 | TRP- 370 | 3.72 | 0 | Hydrophobic |
| C19 | CH2 | TRP- 370 | 4.37 | 0 | Hydrophobic |
| C24 | CZ2 | TRP- 370 | 4.21 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 370 | 3.83 | 0 | Hydrophobic |
| C8 | CB | PRO- 371 | 4.21 | 0 | Hydrophobic |
| C | CB | PRO- 371 | 3.52 | 0 | Hydrophobic |
| C | CE1 | PHE- 372 | 3.37 | 0 | Hydrophobic |
| CL | CG | LYS- 374 | 3.76 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 376 | 4.36 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 376 | 4.42 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 381 | 3.73 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 381 | 3.87 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 383 | 3.46 | 0 | Hydrophobic |
| C27 | CD2 | TYR- 428 | 4.18 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 429 | 3.13 | 163.54 | H-Bond (Protein Donor) |
| C24 | CB | VAL- 435 | 4.22 | 0 | Hydrophobic |
| C23 | CB | VAL- 435 | 4.46 | 0 | Hydrophobic |
| C | CG2 | VAL- 435 | 3.61 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 435 | 4.13 | 0 | Hydrophobic |
| C24 | SD | MET- 438 | 3.85 | 0 | Hydrophobic |
