sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-02-26
| Name: | Oxalyl-CoA decarboxylase |
|---|---|
| ID: | OXC_OXAFO |
| AC: | P40149 |
| Organism: | Oxalobacter formigenes |
| Reign: | Bacteria |
| TaxID: | 847 |
| EC Number: | 4.1.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 31 % |
| B | 69 % |
| B-Factor: | 38.405 |
|---|---|
| Number of residues: | 50 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.112 | 1397.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.41 | 54.59 |
| According to VolSite | |
| HET Code: | TPW |
|---|---|
| Formula: | C13H16N3O7P2S |
| Molecular weight: | 420.295 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 82.52 % |
| Polar Surface area: | 221.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 46.8949 | 3.92985 | 0.8705 |
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 |
| C4A | CG1 | VAL- 31 | 4.1 | 0 | Hydrophobic |
| N1' | OE2 | GLU- 56 | 2.54 | 140.75 | H-Bond (Ligand Donor) |
| C35 | CG1 | VAL- 79 | 3.97 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 79 | 3.93 | 0 | Hydrophobic |
| C2A | CB | PRO- 82 | 4 | 0 | Hydrophobic |
| O23 | OH | TYR- 377 | 2.61 | 125.51 | H-Bond (Protein Donor) |
| S1 | CB | ALA- 401 | 4.02 | 0 | Hydrophobic |
| C5B | CB | ALA- 401 | 3.72 | 0 | Hydrophobic |
| O11 | N | ALA- 401 | 3.1 | 174.87 | H-Bond (Protein Donor) |
| O21 | N | ASN- 402 | 2.9 | 147.29 | H-Bond (Protein Donor) |
| O21 | ND2 | ASN- 402 | 2.81 | 168.86 | H-Bond (Protein Donor) |
| O23 | N | ALA- 403 | 3.15 | 131.15 | H-Bond (Protein Donor) |
| N4' | O | GLY- 426 | 2.84 | 167.74 | H-Bond (Ligand Donor) |
| C2A | CB | MET- 428 | 4.45 | 0 | Hydrophobic |
| S1 | SD | MET- 428 | 4.08 | 0 | Hydrophobic |
| C4A | CG | MET- 428 | 4.21 | 0 | Hydrophobic |
| C5A | CG | MET- 428 | 4.29 | 0 | Hydrophobic |
| C5' | CG | MET- 428 | 4.12 | 0 | Hydrophobic |
| N3' | N | MET- 428 | 3.38 | 167.67 | H-Bond (Protein Donor) |
| O13 | N | SER- 453 | 2.97 | 159.39 | H-Bond (Protein Donor) |
| C5A | CB | SER- 453 | 3.71 | 0 | Hydrophobic |
| O12 | N | ALA- 454 | 2.9 | 159.15 | H-Bond (Protein Donor) |
| C2A | CE2 | PHE- 457 | 3.68 | 0 | Hydrophobic |
| C4A | CZ | PHE- 457 | 4.06 | 0 | Hydrophobic |
| O22 | ND2 | ASN- 479 | 3.25 | 127.94 | H-Bond (Protein Donor) |
| C4A | CD1 | ILE- 482 | 4.45 | 0 | Hydrophobic |
| C5B | CG2 | ILE- 482 | 3.64 | 0 | Hydrophobic |
| C5B | CE2 | TYR- 483 | 4.31 | 0 | Hydrophobic |
| O22 | N | TYR- 483 | 3.33 | 124.89 | H-Bond (Protein Donor) |
| O13 | MG | MG- 1555 | 2.06 | 0 | Metal Acceptor |
| O22 | MG | MG- 1555 | 2.04 | 0 | Metal Acceptor |
| O23 | O | HOH- 2269 | 2.87 | 140.96 | H-Bond (Protein Donor) |
