sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.020 Å
X-ray
2011-01-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.380 | 8.380 | 8.380 | 0.000 | 8.380 | 1 |
| Name: | Bcl-2-like protein 1 |
|---|---|
| ID: | B2CL1_HUMAN |
| AC: | Q07817 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.426 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.925 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.16 | 37.84 |
| According to VolSite | |
| HET Code: | HI0 |
|---|---|
| Formula: | C43H47ClN8O4S2 |
| Molecular weight: | 839.467 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.19 % |
| Polar Surface area: | 175.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 7 |
| Aromatic rings: | 6 |
| Anionic atoms: | 1 |
| Cationic atoms: | 3 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 16 |
| X | Y | Z |
|---|---|---|
| -9.83836 | -14.1711 | 10.8081 |
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 |
| C43 | CB | ALA- 93 | 4.45 | 0 | Hydrophobic |
| C33 | CG | GLU- 96 | 4.39 | 0 | Hydrophobic |
| S2 | CG | GLU- 96 | 3.33 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 97 | 4.05 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 97 | 4.22 | 0 | Hydrophobic |
| C43 | CB | PHE- 97 | 3.76 | 0 | Hydrophobic |
| C42 | CB | PHE- 97 | 3.79 | 0 | Hydrophobic |
| C39 | CD | ARG- 100 | 4.44 | 0 | Hydrophobic |
| S2 | CD | ARG- 100 | 3.98 | 0 | Hydrophobic |
| C3 | CD1 | TYR- 101 | 3.79 | 0 | Hydrophobic |
| C19 | CZ | TYR- 101 | 3.45 | 0 | Hydrophobic |
| N3 | OH | TYR- 101 | 2.56 | 168.48 | H-Bond (Ligand Donor) |
| C17 | CB | ALA- 104 | 4.33 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 105 | 3.33 | 0 | Hydrophobic |
| C16 | CB | LEU- 108 | 4.07 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 108 | 4.15 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 126 | 3.69 | 0 | Hydrophobic |
| C8 | CG | GLU- 129 | 3.84 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 130 | 3.8 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 130 | 4.33 | 0 | Hydrophobic |
| C9 | CB | LEU- 130 | 3.63 | 0 | Hydrophobic |
| O2 | N | GLY- 138 | 3.07 | 150.68 | H-Bond (Protein Donor) |
| C4 | CG | ARG- 139 | 4.44 | 0 | Hydrophobic |
| C20 | CG | ARG- 139 | 3.74 | 0 | Hydrophobic |
| C42 | CB | VAL- 141 | 3.78 | 0 | Hydrophobic |
| C43 | CG1 | VAL- 141 | 4.26 | 0 | Hydrophobic |
| C4 | CB | ALA- 142 | 4.23 | 0 | Hydrophobic |
| C13 | CB | ALA- 142 | 3.97 | 0 | Hydrophobic |
| CL1 | CB | SER- 145 | 4.17 | 0 | Hydrophobic |
| C14 | CB | PHE- 146 | 3.71 | 0 | Hydrophobic |
| CL1 | CB | ALA- 149 | 4.48 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 195 | 3.96 | 0 | Aromatic Face/Face |
