sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 Å
X-ray
2012-02-26
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 29.688 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.113 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 57.79 | 42.21 |
| According to VolSite | |
| HET Code: | S5B |
|---|---|
| Formula: | C25H24N3O3 |
| Molecular weight: | 414.476 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43 % |
| Polar Surface area: | 91.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 44.1026 | 3.37829 | 1.54445 |
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 |
| C01 | CB | PRO- 98 | 4.26 | 0 | Hydrophobic |
| C09 | CB | PRO- 98 | 4.32 | 0 | Hydrophobic |
| C24 | CB | PRO- 98 | 4.11 | 0 | Hydrophobic |
| C12 | CG | PRO- 98 | 4.27 | 0 | Hydrophobic |
| C01 | CE1 | PHE- 99 | 3.44 | 0 | Hydrophobic |
| C01 | CG2 | VAL- 103 | 4.36 | 0 | Hydrophobic |
| C04 | CG1 | VAL- 103 | 4.33 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 103 | 4.37 | 0 | Hydrophobic |
| O1 | NZ | LYS- 107 | 3.43 | 122.96 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 107 | 3.43 | 0 | Ionic (Protein Cationic) |
| C18 | CD2 | LEU- 108 | 4.24 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 108 | 3.65 | 0 | Hydrophobic |
| C09 | CD1 | LEU- 108 | 3.71 | 0 | Hydrophobic |
| C04 | CD1 | LEU- 110 | 3.71 | 0 | Hydrophobic |
| C04 | CE1 | TYR- 113 | 4.34 | 0 | Hydrophobic |
| C04 | CD2 | TYR- 155 | 3.91 | 0 | Hydrophobic |
| O01 | ND2 | ASN- 156 | 3.25 | 167.96 | H-Bond (Protein Donor) |
| C01 | CG1 | ILE- 162 | 3.83 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 162 | 4.12 | 0 | Hydrophobic |
| C07 | CG1 | ILE- 162 | 3.88 | 0 | Hydrophobic |
| C08 | CD1 | ILE- 162 | 4.34 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 162 | 4.19 | 0 | Hydrophobic |
| C13 | SD | MET- 165 | 4.15 | 0 | Hydrophobic |
