sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-03-03
| Name: | Shikimate kinase |
|---|---|
| ID: | AROK_MYCTU |
| AC: | P9WPY3 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.7.1.71 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 9 % |
| C | 77 % |
| D | 14 % |
| B-Factor: | 37.102 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ADP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.951 | 1576.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.54 | 61.46 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.03 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 16.0458 | 19.3393 | 48.731 |
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 |
| O3B | N | GLY- 12 | 2.76 | 137.96 | H-Bond (Protein Donor) |
| O3B | N | GLY- 14 | 3.37 | 156.49 | H-Bond (Protein Donor) |
| O3A | N | GLY- 14 | 3.15 | 127.63 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 15 | 3.99 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 15 | 2.94 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 15 | 2.94 | 149.83 | H-Bond (Protein Donor) |
| O1B | N | SER- 16 | 2.58 | 136.44 | H-Bond (Protein Donor) |
| O2A | N | SER- 16 | 3.36 | 125.41 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 17 | 2.54 | 169.83 | H-Bond (Protein Donor) |
| O2A | N | THR- 17 | 2.74 | 137.12 | H-Bond (Protein Donor) |
| C2' | CB | THR- 17 | 4.14 | 0 | Hydrophobic |
| C1' | CD | ARG- 110 | 4.15 | 0 | Hydrophobic |
| C4' | CB | ARG- 110 | 3.85 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 110 | 3.54 | 13.31 | Pi/Cation |
| N6 | O | ARG- 153 | 3.36 | 164.44 | H-Bond (Ligand Donor) |
| C3' | C3' | ADP- 183 | 4.26 | 0 | Hydrophobic |
| C2' | C2' | ADP- 183 | 4.3 | 0 | Hydrophobic |
| O2' | O3' | ADP- 183 | 2.91 | 153.14 | H-Bond (Ligand Donor) |
| O2B | MG | MG- 202 | 2.06 | 0 | Metal Acceptor |
