sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2013-06-02
| Name: | Shikimate kinase |
|---|---|
| ID: | AROK_MYCTO |
| AC: | P9WPY2 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83331 |
| EC Number: | 2.7.1.71 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 27.116 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | ADP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.004 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 40.58 | 59.42 |
| According to VolSite | |
| HET Code: | K2Q |
|---|---|
| Formula: | C10H11O5 |
| Molecular weight: | 211.191 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.21 % |
| Polar Surface area: | 89.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -12.1158 | -1.41973 | 76.8607 |
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 |
| OAC | OD1 | ASP- 34 | 2.53 | 163.65 | H-Bond (Ligand Donor) |
| OAC | OD2 | ASP- 34 | 3 | 128.36 | H-Bond (Ligand Donor) |
| CAH | CG2 | ILE- 45 | 3.98 | 0 | Hydrophobic |
| CAN | CG2 | ILE- 45 | 4 | 0 | Hydrophobic |
| CAN | CE2 | PHE- 49 | 4.17 | 0 | Hydrophobic |
| CAI | CE2 | PHE- 57 | 4.23 | 0 | Hydrophobic |
| CAN | CZ | PHE- 57 | 4.33 | 0 | Hydrophobic |
| OAA | CZ | ARG- 58 | 3.91 | 0 | Ionic (Protein Cationic) |
| OAA | NH2 | ARG- 58 | 2.91 | 158.15 | H-Bond (Protein Donor) |
| OAD | N | GLY- 80 | 3.06 | 163.69 | H-Bond (Protein Donor) |
| OAA | NH1 | ARG- 136 | 3.26 | 134.92 | H-Bond (Protein Donor) |
| OAA | NH2 | ARG- 136 | 2.94 | 148.62 | H-Bond (Protein Donor) |
| OAB | NH1 | ARG- 136 | 2.75 | 164.83 | H-Bond (Protein Donor) |
| OAA | CZ | ARG- 136 | 3.52 | 0 | Ionic (Protein Cationic) |
| OAB | CZ | ARG- 136 | 3.74 | 0 | Ionic (Protein Cationic) |
| OAC | O | HOH- 2020 | 2.78 | 179.97 | H-Bond (Protein Donor) |
