sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2013-07-30
| Name: | Glucokinase regulatory protein |
|---|---|
| ID: | GCKR_HUMAN |
| AC: | Q14397 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.069 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.234 | 897.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | 1YY |
|---|---|
| Formula: | C23H31F3N3O4S2 |
| Molecular weight: | 534.635 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.45 % |
| Polar Surface area: | 111.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 37.4617 | -23.3961 | 16.6096 |
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 |
| C22 | CG1 | VAL- 10 | 4.29 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 10 | 4.3 | 0 | Hydrophobic |
| C20 | CB | ILE- 11 | 4.21 | 0 | Hydrophobic |
| C19 | CG1 | ILE- 11 | 3.96 | 0 | Hydrophobic |
| O4 | N | ILE- 11 | 2.85 | 166.79 | H-Bond (Protein Donor) |
| C20 | CZ | TYR- 24 | 3.93 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 28 | 3.56 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 28 | 3.57 | 0 | Hydrophobic |
| C2 | CG | PRO- 29 | 4.03 | 0 | Hydrophobic |
| C2 | CG | GLU- 32 | 4.37 | 0 | Hydrophobic |
| S2 | CG | GLU- 32 | 4.48 | 0 | Hydrophobic |
| C4 | CG | GLU- 32 | 3.64 | 0 | Hydrophobic |
| C15 | CB | GLU- 32 | 3.6 | 0 | Hydrophobic |
| F2 | CB | SER- 34 | 4 | 0 | Hydrophobic |
| S2 | CB | SER- 183 | 4.12 | 0 | Hydrophobic |
| S2 | CD | ARG- 215 | 4.08 | 0 | Hydrophobic |
| F3 | CB | SER- 255 | 4.16 | 0 | Hydrophobic |
| S2 | CD | LYS- 514 | 4.16 | 0 | Hydrophobic |
| C1 | CB | TRP- 517 | 4.08 | 0 | Hydrophobic |
| C4 | CB | ARG- 518 | 4.29 | 0 | Hydrophobic |
| C15 | CG | ARG- 518 | 4.39 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 520 | 4.46 | 0 | Hydrophobic |
| C22 | CB | ALA- 521 | 4.24 | 0 | Hydrophobic |
| C17 | CB | ALA- 521 | 4.01 | 0 | Hydrophobic |
| C13 | CB | ALA- 521 | 3.53 | 0 | Hydrophobic |
| C17 | CG | MET- 522 | 4.06 | 0 | Hydrophobic |
| F2 | CD | ARG- 525 | 4.25 | 0 | Hydrophobic |
| C17 | CB | ARG- 525 | 4.28 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 525 | 3.18 | 149.42 | H-Bond (Protein Donor) |
| O3 | NE | ARG- 525 | 3.19 | 152.56 | H-Bond (Protein Donor) |
| O3 | O | HOH- 848 | 2.61 | 154.24 | H-Bond (Ligand Donor) |
