sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2012-07-23
| Name: | Alpha/beta hydrolase fold protein |
|---|---|
| ID: | D2J2T6_9RHIZ |
| AC: | D2J2T6 |
| Organism: | Ochrobactrum sp. T63 |
| Reign: | Bacteria |
| TaxID: | 680275 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 11.692 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.602 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 69.67 | 30.33 |
| According to VolSite | |
| HET Code: | HL6 |
|---|---|
| Formula: | C10H17NO3 |
| Molecular weight: | 199.247 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.66 % |
| Polar Surface area: | 55.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 39.5394 | 67.2526 | 18.0088 |
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 |
| O1 | N | ASN- 33 | 2.81 | 172.83 | H-Bond (Protein Donor) |
| O3 | ND2 | ASN- 33 | 2.97 | 169.32 | H-Bond (Protein Donor) |
| C7 | CE | MET- 77 | 3.92 | 0 | Hydrophobic |
| O1 | N | LEU- 103 | 2.82 | 176.57 | H-Bond (Protein Donor) |
| C6 | CB | LEU- 103 | 4.32 | 0 | Hydrophobic |
| C6 | CZ | PHE- 138 | 4.48 | 0 | Hydrophobic |
| C8 | CZ | PHE- 138 | 3.74 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 138 | 3.69 | 0 | Hydrophobic |
| C8 | CE | MET- 144 | 3.66 | 0 | Hydrophobic |
| C2 | CG2 | THR- 164 | 3.74 | 0 | Hydrophobic |
| C7 | SD | MET- 188 | 3.99 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 189 | 3.38 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 192 | 3.53 | 0 | Hydrophobic |
| C2 | CD2 | PHE- 221 | 4.17 | 0 | Hydrophobic |
| C3 | CG | PHE- 221 | 4.48 | 0 | Hydrophobic |
| N | O | HOH- 493 | 3.02 | 165.73 | H-Bond (Ligand Donor) |
