sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.290 Å
X-ray
2013-02-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.390 | 8.390 | 8.390 | 0.000 | 8.390 | 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: | 19.001 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.063 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 63.87 | 36.13 |
| According to VolSite | |
| HET Code: | H0Y |
|---|---|
| Formula: | C23H17N4O2S |
| Molecular weight: | 413.472 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.54 % |
| Polar Surface area: | 118.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -18.5636 | -12.2987 | 12.8084 |
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 |
| S9 | CZ | PHE- 97 | 3.72 | 0 | Hydrophobic |
| C6 | CD | ARG- 102 | 4.03 | 0 | Hydrophobic |
| C4 | CG | ARG- 102 | 3.92 | 0 | Hydrophobic |
| C13 | CB | PHE- 105 | 4.39 | 0 | Hydrophobic |
| C18 | CD1 | PHE- 105 | 3.29 | 0 | Hydrophobic |
| C17 | CB | PHE- 105 | 4.19 | 0 | Hydrophobic |
| N10 | O | SER- 106 | 2.76 | 141.89 | H-Bond (Ligand Donor) |
| C13 | CD1 | LEU- 108 | 4.17 | 0 | Hydrophobic |
| N7 | N | LEU- 108 | 2.85 | 172.73 | H-Bond (Protein Donor) |
| C6 | CG2 | THR- 109 | 3.86 | 0 | Hydrophobic |
| C15 | CB | GLU- 129 | 4.44 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 130 | 4.07 | 0 | Hydrophobic |
| S9 | CD2 | LEU- 130 | 3.98 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 130 | 3.54 | 0 | Hydrophobic |
| C21 | CD | ARG- 132 | 4.33 | 0 | Hydrophobic |
| C15 | CD | ARG- 132 | 4.28 | 0 | Hydrophobic |
| O82 | ND2 | ASN- 136 | 3.43 | 161.69 | H-Bond (Protein Donor) |
| O82 | CZ | ARG- 139 | 3.41 | 0 | Ionic (Protein Cationic) |
| O82 | NH2 | ARG- 139 | 3.11 | 127.82 | H-Bond (Protein Donor) |
| O82 | NE | ARG- 139 | 2.95 | 132.56 | H-Bond (Protein Donor) |
| C27 | CG | ARG- 139 | 3.97 | 0 | Hydrophobic |
| C20 | CG | ARG- 139 | 4.24 | 0 | Hydrophobic |
| S9 | CB | ALA- 142 | 4.24 | 0 | Hydrophobic |
| C27 | CB | ALA- 142 | 3.72 | 0 | Hydrophobic |
| C3 | CB | SER- 145 | 4.1 | 0 | Hydrophobic |
| C3 | CB | PHE- 146 | 3.77 | 0 | Hydrophobic |
| C1 | CB | ALA- 149 | 3.71 | 0 | Hydrophobic |
