sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2013-02-04
| 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: | 77.161 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.456 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.49 | 44.51 |
| According to VolSite | |
| HET Code: | X8U |
|---|---|
| Formula: | C31H27N4O2S2 |
| Molecular weight: | 551.702 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.78 % |
| Polar Surface area: | 146.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 14.1432 | -32.8285 | 9.57336 |
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 |
| C29 | CB | ALA- 93 | 3.86 | 0 | Hydrophobic |
| C30 | CB | GLU- 96 | 3.71 | 0 | Hydrophobic |
| S1 | CZ | PHE- 97 | 4.01 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 97 | 3.79 | 0 | Hydrophobic |
| C25 | CD1 | PHE- 97 | 3.49 | 0 | Hydrophobic |
| C31 | CB | PHE- 97 | 3.66 | 0 | Hydrophobic |
| C23 | CG | TYR- 101 | 4.46 | 0 | Hydrophobic |
| C31 | CE2 | TYR- 101 | 3.48 | 0 | Hydrophobic |
| C24 | CD2 | TYR- 101 | 3.85 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 105 | 4.45 | 0 | Hydrophobic |
| C9 | CB | PHE- 105 | 4.13 | 0 | Hydrophobic |
| C14 | CD1 | PHE- 105 | 3.35 | 0 | Hydrophobic |
| C13 | CB | PHE- 105 | 4.12 | 0 | Hydrophobic |
| C9 | CB | SER- 106 | 4.45 | 0 | Hydrophobic |
| N2 | O | SER- 106 | 2.79 | 135.74 | H-Bond (Ligand Donor) |
| C9 | CG | LEU- 108 | 3.8 | 0 | Hydrophobic |
| N1 | N | LEU- 108 | 3.02 | 171.77 | H-Bond (Protein Donor) |
| C1 | CG2 | THR- 109 | 3.76 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 130 | 4.35 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 130 | 3.54 | 0 | Hydrophobic |
| C11 | CD | ARG- 132 | 4.35 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 136 | 3.47 | 125.02 | H-Bond (Protein Donor) |
| O1 | ND2 | ASN- 136 | 3.11 | 151.54 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 139 | 3.55 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 139 | 3.24 | 137.64 | H-Bond (Protein Donor) |
| O1 | NE | ARG- 139 | 3.01 | 150.27 | H-Bond (Protein Donor) |
| N4 | NE | ARG- 139 | 3.29 | 132.77 | H-Bond (Protein Donor) |
| C22 | CG | ARG- 139 | 4.5 | 0 | Hydrophobic |
| S2 | CG | ARG- 139 | 4.27 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 141 | 4.16 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 141 | 3.99 | 0 | Hydrophobic |
| S2 | CB | ALA- 142 | 3.84 | 0 | Hydrophobic |
| S1 | CB | ALA- 142 | 4.33 | 0 | Hydrophobic |
| C3 | CB | SER- 145 | 4.03 | 0 | Hydrophobic |
| C3 | CB | PHE- 146 | 3.8 | 0 | Hydrophobic |
| C1 | CB | ALA- 149 | 3.7 | 0 | Hydrophobic |
