sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2014-08-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 1 |
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 37.948 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.231 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 58.82 | 41.18 |
| According to VolSite | |
| HET Code: | 73B |
|---|---|
| Formula: | C25H22ClN2O3 |
| Molecular weight: | 433.907 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.51 % |
| Polar Surface area: | 72.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -33.3191 | -20.2471 | 16.5881 |
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 |
| CL1 | CZ2 | TRP- 370 | 3.92 | 0 | Hydrophobic |
| C18 | CB | PRO- 371 | 4.1 | 0 | Hydrophobic |
| C7 | CG | PRO- 371 | 4.35 | 0 | Hydrophobic |
| C12 | CB | PRO- 371 | 4.34 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 372 | 3.51 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 376 | 4.07 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 376 | 3.7 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 376 | 4.48 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 381 | 4.44 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 381 | 3.93 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 381 | 4.07 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 383 | 3.41 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 386 | 4.25 | 0 | Hydrophobic |
| C18 | SG | CYS- 425 | 4.11 | 0 | Hydrophobic |
| C1 | CD2 | TYR- 428 | 4.28 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 429 | 3.09 | 149.53 | H-Bond (Protein Donor) |
| CL1 | CB | ASP- 434 | 4.01 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 435 | 4.16 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 435 | 3.56 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 435 | 3.89 | 0 | Hydrophobic |
| C6 | CB | VAL- 435 | 3.67 | 0 | Hydrophobic |
| CL1 | SD | MET- 438 | 3.97 | 0 | Hydrophobic |
| C7 | SD | MET- 438 | 3.92 | 0 | Hydrophobic |
