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
2003-02-04
| Name: | Shikimate dehydrogenase (NADP(+)) |
|---|---|
| ID: | AROE_METJA |
| AC: | Q58484 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 39.267 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.367 | 1171.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.28 | 50.72 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 56.64 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -14.4052 | -11.5131 | 55.8022 |
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 | ALA- 136 | 2.7 | 148.67 | H-Bond (Protein Donor) |
| O3 | N | GLY- 138 | 3.42 | 132.93 | H-Bond (Protein Donor) |
| O2N | N | ALA- 139 | 2.65 | 152.62 | H-Bond (Protein Donor) |
| C5D | CB | ALA- 139 | 4.12 | 0 | Hydrophobic |
| C5N | CB | ALA- 139 | 4.07 | 0 | Hydrophobic |
| O1X | CZ | ARG- 158 | 2.9 | 0 | Ionic (Protein Cationic) |
| DuAr | CZ | ARG- 158 | 3.98 | 157.9 | Pi/Cation |
| O2X | N | THR- 159 | 3.36 | 129.95 | H-Bond (Protein Donor) |
| O2X | OG1 | THR- 159 | 2.65 | 155.86 | H-Bond (Protein Donor) |
| O3X | NZ | LYS- 162 | 2.57 | 160.03 | H-Bond (Protein Donor) |
| O3X | NZ | LYS- 162 | 2.57 | 0 | Ionic (Protein Cationic) |
| C1B | CG2 | THR- 201 | 4.4 | 0 | Hydrophobic |
| C3D | CG | PRO- 202 | 4.13 | 0 | Hydrophobic |
| C2D | CE | MET- 205 | 4.25 | 0 | Hydrophobic |
| N7N | O | LEU- 229 | 2.91 | 144.91 | H-Bond (Ligand Donor) |
| N7N | O | GLY- 252 | 3.06 | 161.26 | H-Bond (Ligand Donor) |
| C3N | SD | MET- 255 | 3.73 | 0 | Hydrophobic |
| C4N | CE | MET- 255 | 3.65 | 0 | Hydrophobic |
