sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.080 Å
X-ray
2013-02-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.770 | 5.820 | 5.920 | 0.840 | 6.690 | 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: | 11.221 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.185 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.23 | 40.77 |
| According to VolSite | |
| HET Code: | 1K0 |
|---|---|
| Formula: | C20H22N2O5 |
| Molecular weight: | 370.399 g/mol |
| DrugBank ID: | DB12000 |
| Buried Surface Area: | 39.23 % |
| Polar Surface area: | 89.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 10.3791 | 22.0594 | -3.1667 |
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 |
| C1 | CZ3 | TRP- 370 | 3.76 | 0 | Hydrophobic |
| C1 | CB | PRO- 371 | 4.47 | 0 | Hydrophobic |
| C3 | CB | PRO- 371 | 3.72 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 372 | 3.51 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 376 | 3.7 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 376 | 3.7 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 381 | 4.5 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 381 | 3.59 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 383 | 3.92 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 383 | 3.75 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 383 | 3.73 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 383 | 3.7 | 0 | Hydrophobic |
| N1 | OD1 | ASN- 429 | 2.95 | 148.93 | H-Bond (Ligand Donor) |
| O5 | ND2 | ASN- 429 | 2.84 | 165.43 | H-Bond (Protein Donor) |
| C5 | CG2 | VAL- 435 | 4.16 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 435 | 3.75 | 0 | Hydrophobic |
