sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.920 Å
X-ray
2011-01-01
| Name: | 2-oxopropyl-CoM reductase, carboxylating |
|---|---|
| ID: | XECC_XANP2 |
| AC: | Q56839 |
| Organism: | Xanthobacter autotrophicus |
| Reign: | Bacteria |
| TaxID: | 78245 |
| EC Number: | 1.8.1.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 79 % |
| B | 21 % |
| B-Factor: | 17.845 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.699 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 71.60 | 28.40 |
| According to VolSite | |
| HET Code: | KPC |
|---|---|
| Formula: | C5H9O4S2 |
| Molecular weight: | 197.253 g/mol |
| DrugBank ID: | DB03163 |
| Buried Surface Area: | 82.58 % |
| Polar Surface area: | 107.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -20.2472 | 1.756 | 13.5068 |
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 |
| OAL | CZ | ARG- 56 | 3.72 | 0 | Ionic (Protein Cationic) |
| OAB | CZ | ARG- 56 | 3.57 | 0 | Ionic (Protein Cationic) |
| OAL | NE | ARG- 56 | 2.77 | 163.5 | H-Bond (Protein Donor) |
| OAB | NE | ARG- 56 | 3.48 | 130.08 | H-Bond (Protein Donor) |
| OAB | NH2 | ARG- 56 | 2.81 | 155.13 | H-Bond (Protein Donor) |
| SAH | CB | CYS- 82 | 3.65 | 0 | Hydrophobic |
| CAG | SG | CYS- 82 | 3.55 | 0 | Hydrophobic |
| CAF | CB | CYS- 82 | 4.32 | 0 | Hydrophobic |
| CAI | CB | PRO- 83 | 3.89 | 0 | Hydrophobic |
| SAH | CG2 | VAL- 88 | 3.95 | 0 | Hydrophobic |
| CAK | CB | PRO- 136 | 3.72 | 0 | Hydrophobic |
| CAI | CB | PRO- 136 | 4.31 | 0 | Hydrophobic |
| CAK | CE | MET- 140 | 3.55 | 0 | Hydrophobic |
| CAI | SD | MET- 140 | 4.31 | 0 | Hydrophobic |
| CAF | SD | MET- 140 | 3.85 | 0 | Hydrophobic |
| CAG | CE | MET- 361 | 3.95 | 0 | Hydrophobic |
| OAD | NE | ARG- 365 | 3.02 | 152.99 | H-Bond (Protein Donor) |
| OAD | NH2 | ARG- 365 | 3.09 | 145.64 | H-Bond (Protein Donor) |
| OAB | NH2 | ARG- 365 | 3.49 | 136.21 | H-Bond (Protein Donor) |
| OAD | CZ | ARG- 365 | 3.5 | 0 | Ionic (Protein Cationic) |
| CAK | CD1 | LEU- 431 | 3.62 | 0 | Hydrophobic |
| SAH | CE2 | PHE- 501 | 3.75 | 0 | Hydrophobic |
| CAG | CZ | PHE- 501 | 3.73 | 0 | Hydrophobic |
