sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2001-07-02
| Name: | Homoserine kinase |
|---|---|
| ID: | KHSE_METJA |
| AC: | Q58504 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 2.7.1.39 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 25.114 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.740 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.55 | 55.45 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.29 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 62.1685 | 37.6786 | 20.5527 |
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 |
| N6 | OD1 | ASN- 62 | 3.05 | 164.49 | H-Bond (Ligand Donor) |
| N7 | N | VAL- 63 | 3.06 | 158.59 | H-Bond (Protein Donor) |
| N1 | NZ | LYS- 87 | 2.75 | 159.14 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 91 | 3.59 | 0 | Hydrophobic |
| O2A | N | GLY- 92 | 2.57 | 154.23 | H-Bond (Protein Donor) |
| O1G | N | GLY- 96 | 2.55 | 147.48 | H-Bond (Protein Donor) |
| O1A | OG | SER- 98 | 2.62 | 143.39 | H-Bond (Protein Donor) |
| C5' | CB | SER- 98 | 4.25 | 0 | Hydrophobic |
| N6 | OG | SER- 101 | 2.98 | 140.8 | H-Bond (Ligand Donor) |
| C1' | CB | SER- 133 | 4.27 | 0 | Hydrophobic |
| C4' | CB | SER- 133 | 3.88 | 0 | Hydrophobic |
| N3B | OG1 | THR- 183 | 3.04 | 120.5 | H-Bond (Ligand Donor) |
| O2G | N | SER- 261 | 3.31 | 177.28 | H-Bond (Protein Donor) |
| N3B | O | HOH- 2263 | 3.02 | 127.78 | H-Bond (Ligand Donor) |
| O3G | O | HOH- 2303 | 2.86 | 179.95 | H-Bond (Protein Donor) |
| O2A | O | HOH- 2305 | 2.91 | 179.97 | H-Bond (Protein Donor) |
