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
2014-08-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 1 |
| 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 | 39 % |
| C | 61 % |
| B-Factor: | 21.307 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.422 | 948.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.74 | 46.26 |
| According to VolSite | |
| HET Code: | 73B |
|---|---|
| Formula: | C25H22ClN2O3 |
| Molecular weight: | 433.907 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.68 % |
| Polar Surface area: | 72.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 2.85974 | 7.74948 | 18.8102 |
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 |
| CL1 | CB | ASN- 77 | 4.18 | 0 | Hydrophobic |
| C7 | CB | ASN- 77 | 3.69 | 0 | Hydrophobic |
| C21 | CB | GLN- 80 | 4.12 | 0 | Hydrophobic |
| C23 | CD | LYS- 84 | 4.19 | 0 | Hydrophobic |
| C22 | CB | LYS- 84 | 3.86 | 0 | Hydrophobic |
| CL1 | CZ2 | TRP- 97 | 3.61 | 0 | Hydrophobic |
| C18 | CB | PRO- 98 | 4.25 | 0 | Hydrophobic |
| C9 | CG | PRO- 98 | 4.28 | 0 | Hydrophobic |
| C14 | CB | PRO- 98 | 4.02 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 99 | 3.8 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 103 | 4.3 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 103 | 3.93 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 103 | 4.17 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 108 | 3.88 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 108 | 3.92 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 110 | 3.65 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 113 | 4.4 | 0 | Hydrophobic |
| C1 | CD2 | TYR- 155 | 4.21 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 156 | 3.12 | 156.65 | H-Bond (Protein Donor) |
| CL1 | CB | ASP- 161 | 3.93 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 162 | 4.34 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 162 | 3.95 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 162 | 3.71 | 0 | Hydrophobic |
| CL1 | SD | MET- 165 | 4.25 | 0 | Hydrophobic |
| C9 | SD | MET- 165 | 3.84 | 0 | Hydrophobic |
| CL1 | CG | PRO- 181 | 3.41 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 187 | 3.94 | 0 | Hydrophobic |
| O2 | O | HOH- 2020 | 2.86 | 179.98 | H-Bond (Protein Donor) |
