sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.770 Å
X-ray
2013-11-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.430 | 6.430 | 6.430 | 0.000 | 6.430 | 1 |
| Name: | Endoplasmin |
|---|---|
| ID: | ENPL_HUMAN |
| AC: | P14625 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 59.130 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.447 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 66.67 | 33.33 |
| According to VolSite | |
| HET Code: | 2LC |
|---|---|
| Formula: | C22H26FN3O3 |
| Molecular weight: | 399.459 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.37 % |
| Polar Surface area: | 86.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -19.6277 | -33.0514 | -8.01428 |
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 |
| C28 | CB | ASN- 107 | 3.62 | 0 | Hydrophobic |
| C23 | CB | ASP- 110 | 4.16 | 0 | Hydrophobic |
| C21 | CD | LYS- 114 | 4.42 | 0 | Hydrophobic |
| N26 | OD2 | ASP- 149 | 3.14 | 135.9 | H-Bond (Ligand Donor) |
| C21 | CG1 | VAL- 152 | 4.48 | 0 | Hydrophobic |
| C20 | CG | MET- 154 | 4.23 | 0 | Hydrophobic |
| C15 | SD | MET- 154 | 4.13 | 0 | Hydrophobic |
| C28 | CE | MET- 154 | 3.94 | 0 | Hydrophobic |
| C11 | SD | MET- 154 | 3.83 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 159 | 3.91 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 159 | 3.97 | 0 | Hydrophobic |
| C11 | CB | ASN- 162 | 3.69 | 0 | Hydrophobic |
| C12 | CZ | PHE- 199 | 4.01 | 0 | Hydrophobic |
| C13 | CD2 | PHE- 199 | 4.1 | 0 | Hydrophobic |
| C30 | CB | PHE- 199 | 4.37 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 199 | 3.7 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 200 | 4.33 | 0 | Hydrophobic |
| C9 | CZ | TYR- 200 | 4.45 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 211 | 3.84 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 223 | 4.03 | 0 | Hydrophobic |
| C12 | CD2 | TRP- 223 | 3.5 | 0 | Hydrophobic |
| F29 | CD1 | ILE- 247 | 3.24 | 0 | Hydrophobic |
