sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2015-06-17
| Name: | Ribokinase |
|---|---|
| ID: | RBSK_HUMAN |
| AC: | Q9H477 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.689 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.866 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | ACP |
|---|---|
| Formula: | C11H14N5O12P3 |
| Molecular weight: | 501.176 g/mol |
| DrugBank ID: | DB03909 |
| Buried Surface Area: | 60.8 % |
| Polar Surface area: | 310.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 4.129 | 58.5836 | -19.1186 |
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 |
| O2A | OG1 | THR- 235 | 2.72 | 161.02 | H-Bond (Protein Donor) |
| C3' | CB | THR- 235 | 4.33 | 0 | Hydrophobic |
| C5' | CB | THR- 235 | 3.92 | 0 | Hydrophobic |
| C2' | CG2 | THR- 256 | 4.39 | 0 | Hydrophobic |
| O1G | OG1 | THR- 264 | 2.74 | 169.66 | H-Bond (Protein Donor) |
| C3B | CB | THR- 264 | 4.06 | 0 | Hydrophobic |
| C3B | CB | ALA- 267 | 4.27 | 0 | Hydrophobic |
| C5' | CB | ALA- 267 | 4.14 | 0 | Hydrophobic |
| O1B | N | GLY- 268 | 2.76 | 154.39 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 271 | 4.17 | 0 | Hydrophobic |
| O3' | OD1 | ASN- 295 | 3.34 | 160.38 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASN- 295 | 2.82 | 140.23 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 298 | 3.95 | 0 | Hydrophobic |
| C1' | CB | ALA- 298 | 3.66 | 0 | Hydrophobic |
