sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-03-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.150 | 7.440 | 7.280 | 0.360 | 8.050 | 4 |
| 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: | 25.055 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.182 | 391.500 |
| % Hydrophobic | % Polar |
|---|---|
| 68.97 | 31.03 |
| According to VolSite | |
| HET Code: | 1GH |
|---|---|
| Formula: | C23H21N5O3 |
| Molecular weight: | 415.445 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.38 % |
| Polar Surface area: | 93.38 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: | 4 |
| X | Y | Z |
|---|---|---|
| 12.1475 | -5.77406 | 19.8636 |
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 |
| C17 | CB | PRO- 52 | 4.16 | 0 | Hydrophobic |
| C10 | CG | PRO- 52 | 3.83 | 0 | Hydrophobic |
| C4 | CB | PRO- 52 | 4.14 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 53 | 3.48 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 57 | 4.22 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 57 | 4.27 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 57 | 4.12 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 62 | 3.97 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 62 | 3.77 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 62 | 3.83 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 62 | 3.95 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 64 | 3.24 | 0 | Hydrophobic |
| C23 | CE1 | TYR- 67 | 4.44 | 0 | Hydrophobic |
| C23 | CD2 | TYR- 109 | 4.05 | 0 | Hydrophobic |
| O3 | ND2 | ASN- 110 | 3.25 | 159.91 | H-Bond (Protein Donor) |
| C11 | CB | ASP- 115 | 4.28 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 116 | 4.28 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 116 | 3.82 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 116 | 3.81 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 116 | 3.88 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 116 | 3.8 | 0 | Hydrophobic |
| C11 | SD | MET- 119 | 3.8 | 0 | Hydrophobic |
