sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-04-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.730 | 8.200 | 8.000 | 1.160 | 9.890 | 6 |
| 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: | 37.453 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.852 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.47 | 38.53 |
| According to VolSite | |
| HET Code: | N3C |
|---|---|
| Formula: | C42H47ClN6O5S2 |
| Molecular weight: | 815.443 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.96 % |
| Polar Surface area: | 166.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 1 |
| Cationic atoms: | 3 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 16 |
| X | Y | Z |
|---|---|---|
| -9.87373 | -14.5224 | 10.7994 |
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 |
| S42 | CG | GLU- 96 | 3.51 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 97 | 3.98 | 0 | Hydrophobic |
| C18 | CE2 | PHE- 97 | 4.17 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 97 | 4 | 0 | Hydrophobic |
| C45 | CB | PHE- 97 | 3.97 | 0 | Hydrophobic |
| S42 | CD | ARG- 100 | 4.3 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 101 | 3.61 | 0 | Hydrophobic |
| C3 | CB | ALA- 104 | 4.34 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 105 | 3.36 | 0 | Hydrophobic |
| C2 | CB | LEU- 108 | 4.14 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 108 | 4.29 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 126 | 3.78 | 0 | Hydrophobic |
| C10 | CG | GLU- 129 | 4.08 | 0 | Hydrophobic |
| C9 | CB | GLU- 129 | 4.24 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 130 | 3.79 | 0 | Hydrophobic |
| C9 | CB | LEU- 130 | 3.64 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 130 | 4.4 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 130 | 3.96 | 0 | Hydrophobic |
| O29 | N | GLY- 138 | 3.07 | 150.21 | H-Bond (Protein Donor) |
| C25 | CG | ARG- 139 | 3.82 | 0 | Hydrophobic |
| C45 | CB | VAL- 141 | 3.86 | 0 | Hydrophobic |
| C18 | CB | ALA- 142 | 3.93 | 0 | Hydrophobic |
| C5 | CB | ALA- 142 | 4.06 | 0 | Hydrophobic |
| CL1 | CB | SER- 145 | 4.06 | 0 | Hydrophobic |
| C6 | CB | PHE- 146 | 3.84 | 0 | Hydrophobic |
