sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2013-01-28
| Name: | Halohydrin dehalogenase |
|---|---|
| ID: | Q93D82_RHIRD |
| AC: | Q93D82 |
| Organism: | Rhizobium radiobacter |
| Reign: | Bacteria |
| TaxID: | 358 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.431 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.723 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | 1H1 |
|---|---|
| Formula: | C7H11NO3 |
| Molecular weight: | 157.167 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.19 % |
| Polar Surface area: | 70.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 70.9739 | 33.7264 | 16.4938 |
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 |
| C6 | CE1 | PHE- 12 | 3.57 | 0 | Hydrophobic |
| C1 | CZ2 | TRP- 86 | 3.74 | 0 | Hydrophobic |
| O3 | OG | SER- 132 | 2.84 | 162.46 | H-Bond (Protein Donor) |
| C5 | CB | SER- 132 | 4.32 | 0 | Hydrophobic |
| C2 | CH2 | TRP- 139 | 3.86 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 142 | 4.2 | 0 | Hydrophobic |
| C1 | CG | LEU- 142 | 4.08 | 0 | Hydrophobic |
| O3 | OH | TYR- 145 | 2.68 | 147.52 | H-Bond (Protein Donor) |
| C6 | CB | PRO- 175 | 4.2 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 176 | 3.33 | 136.05 | H-Bond (Protein Donor) |
| C4 | CB | ASN- 176 | 4.15 | 0 | Hydrophobic |
| N | N | VAL- 178 | 3.33 | 164.51 | H-Bond (Protein Donor) |
| C5 | CG | TYR- 186 | 4.07 | 0 | Hydrophobic |
| C6 | CD2 | TYR- 186 | 4.06 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 187 | 4.22 | 0 | Hydrophobic |
| N | O | HOH- 403 | 2.93 | 179.95 | H-Bond (Protein Donor) |
