sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2015-08-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.640 | 7.070 | 7.100 | 0.240 | 7.340 | 8 |
| 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: | 12.103 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.607 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.95 | 44.05 |
| According to VolSite | |
| HET Code: | EAM |
|---|---|
| Formula: | C22H22ClN5O2 |
| Molecular weight: | 423.895 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 38.29 % |
| Polar Surface area: | 81.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -6.36893 | -8.58927 | -4.94283 |
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 |
| C21 | CB | PRO- 371 | 4.07 | 0 | Hydrophobic |
| C12 | CG | PRO- 371 | 3.65 | 0 | Hydrophobic |
| C18 | CB | PRO- 371 | 3.98 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 372 | 3.73 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 376 | 4.31 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 376 | 3.96 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 381 | 4.22 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 383 | 3.79 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 428 | 4.35 | 0 | Hydrophobic |
| N5 | ND2 | ASN- 429 | 3.03 | 161.55 | H-Bond (Protein Donor) |
| N4 | ND2 | ASN- 429 | 3.4 | 148.12 | H-Bond (Protein Donor) |
| CL | CB | ASP- 434 | 3.85 | 0 | Hydrophobic |
| C11 | CB | VAL- 435 | 4.27 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 435 | 3.65 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 435 | 4.34 | 0 | Hydrophobic |
| C7 | CB | VAL- 435 | 3.74 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 435 | 4.22 | 0 | Hydrophobic |
| C11 | SD | MET- 438 | 3.8 | 0 | Hydrophobic |
| CL | CE | MET- 438 | 3.63 | 0 | Hydrophobic |
