sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2011-03-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.280 | 7.280 | 7.280 | 0.000 | 7.280 | 2 |
| 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 | 18 % |
| B | 82 % |
| B-Factor: | 43.007 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.249 | 1026.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.24 | 42.76 |
| According to VolSite | |
| HET Code: | WSH |
|---|---|
| Formula: | C25H21N5O2 |
| Molecular weight: | 423.467 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.08 % |
| Polar Surface area: | 81.4 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: | 5 |
| X | Y | Z |
|---|---|---|
| 1.46631 | 4.87019 | 21.7493 |
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 |
| C16 | CB | ASN- 77 | 3.92 | 0 | Hydrophobic |
| C21 | CG | GLN- 80 | 4.29 | 0 | Hydrophobic |
| C1 | CB | PRO- 98 | 4.39 | 0 | Hydrophobic |
| C19 | CG | PRO- 98 | 3.79 | 0 | Hydrophobic |
| C23 | CB | PRO- 98 | 4.06 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 99 | 3.95 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 103 | 4.17 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 103 | 3.69 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 108 | 4.23 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 108 | 3.84 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 108 | 4.15 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 110 | 3.51 | 0 | Hydrophobic |
| C8 | CG | LEU- 110 | 4.39 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 110 | 3.88 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 155 | 4.36 | 0 | Hydrophobic |
| N2 | ND2 | ASN- 156 | 3.13 | 163.82 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 156 | 2.95 | 126.71 | H-Bond (Ligand Donor) |
| C1 | CD1 | ILE- 162 | 4.44 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 162 | 3.36 | 0 | Hydrophobic |
| C14 | CB | ILE- 162 | 4.06 | 0 | Hydrophobic |
| C18 | SD | MET- 165 | 3.78 | 0 | Hydrophobic |
