sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.230 Å
X-ray
2012-06-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.720 | 6.720 | 6.720 | 0.000 | 6.720 | 1 |
| Name: | Bromodomain testis-specific protein |
|---|---|
| ID: | BRDT_HUMAN |
| AC: | Q58F21 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 46.021 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.242 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 62.50 | 37.50 |
| According to VolSite | |
| HET Code: | JQ1 |
|---|---|
| Formula: | C23H26ClN4O2S |
| Molecular weight: | 457.996 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.55 % |
| Polar Surface area: | 99.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 12.7407 | 7.66919 | -52.5894 |
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 |
| CAB | CZ3 | TRP- 50 | 3.79 | 0 | Hydrophobic |
| CAC | CH2 | TRP- 50 | 3.46 | 0 | Hydrophobic |
| CAA | CB | PRO- 51 | 4.45 | 0 | Hydrophobic |
| SAR | CB | PRO- 51 | 3.94 | 0 | Hydrophobic |
| CAK | CG | PRO- 51 | 3.7 | 0 | Hydrophobic |
| CAA | CE1 | PHE- 52 | 3.72 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 56 | 3.66 | 0 | Hydrophobic |
| CAB | CD1 | LEU- 61 | 4.16 | 0 | Hydrophobic |
| CAC | CD2 | LEU- 61 | 4.1 | 0 | Hydrophobic |
| CAE | CB | LEU- 61 | 3.87 | 0 | Hydrophobic |
| CAF | CD2 | LEU- 61 | 4.25 | 0 | Hydrophobic |
| SAR | CD1 | LEU- 61 | 3.91 | 0 | Hydrophobic |
| CAE | CD2 | LEU- 63 | 3.52 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 63 | 4.2 | 0 | Hydrophobic |
| NAP | ND2 | ASN- 109 | 3.23 | 156.46 | H-Bond (Protein Donor) |
| CLAH | CB | ASP- 114 | 3.44 | 0 | Hydrophobic |
| CAA | CG1 | ILE- 115 | 4.26 | 0 | Hydrophobic |
| CAL | CB | ILE- 115 | 3.98 | 0 | Hydrophobic |
| CAK | CD1 | ILE- 115 | 3.36 | 0 | Hydrophobic |
| CAI | SD | MET- 118 | 3.75 | 0 | Hydrophobic |
