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
2013-07-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.230 | 7.230 | 7.230 | 0.000 | 7.230 | 1 |
| Name: | Apoptosis regulator Bcl-2 |
|---|---|
| ID: | BCL2_HUMAN |
| AC: | P10415 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.971 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.905 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 62.26 | 37.74 |
| According to VolSite | |
| HET Code: | 1XV |
|---|---|
| Formula: | C34H39ClN5O7S |
| Molecular weight: | 697.221 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.41 % |
| Polar Surface area: | 155.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 23.766 | 32.6572 | 10.1639 |
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 |
| C25 | CB | ASP- 100 | 4.42 | 0 | Hydrophobic |
| CL4 | CE2 | PHE- 101 | 4.29 | 0 | Hydrophobic |
| C27 | CE1 | PHE- 101 | 4.17 | 0 | Hydrophobic |
| C27 | CE2 | TYR- 105 | 3.94 | 0 | Hydrophobic |
| C1 | CB | ASP- 108 | 4.22 | 0 | Hydrophobic |
| CL4 | CD2 | PHE- 109 | 3.7 | 0 | Hydrophobic |
| C9 | CB | MET- 112 | 3.75 | 0 | Hydrophobic |
| C18 | CG | MET- 112 | 4.46 | 0 | Hydrophobic |
| C22 | CE | MET- 112 | 3.89 | 0 | Hydrophobic |
| C1 | CE | MET- 112 | 3.69 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 130 | 3.64 | 0 | Hydrophobic |
| C30 | CG | GLU- 133 | 3.8 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 134 | 4.37 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 134 | 3.97 | 0 | Hydrophobic |
| C30 | CB | LEU- 134 | 4.22 | 0 | Hydrophobic |
| C11 | CB | TRP- 141 | 4.43 | 0 | Hydrophobic |
| O43 | N | GLY- 142 | 2.99 | 150.59 | H-Bond (Protein Donor) |
| C26 | CG | ARG- 143 | 4.36 | 0 | Hydrophobic |
| C5 | CG | ARG- 143 | 3.79 | 0 | Hydrophobic |
| C26 | CB | ALA- 146 | 4.36 | 0 | Hydrophobic |
| C2 | CB | ALA- 146 | 4.14 | 0 | Hydrophobic |
| CL4 | CB | GLU- 149 | 4.06 | 0 | Hydrophobic |
| C10 | CB | PHE- 150 | 3.8 | 0 | Hydrophobic |
| CL4 | CG2 | VAL- 153 | 3.92 | 0 | Hydrophobic |
| C24 | CE1 | TYR- 199 | 3.9 | 0 | Hydrophobic |
