sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2012-07-02
| Name: | Coenzyme A disulfide reductase |
|---|---|
| ID: | CDR_PYRHO |
| AC: | O58308 |
| Organism: | Pyrococcus horikoshii |
| Reign: | Archaea |
| TaxID: | 70601 |
| EC Number: | 1.8.1.14 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 8 % |
| B | 92 % |
| B-Factor: | 59.732 |
|---|---|
| Number of residues: | 64 |
| Including | |
| Standard Amino Acids: | 62 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | COA |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.136 | 1562.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.05 | 47.95 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 72.45 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -33.8669 | -16.9262 | -9.68374 |
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 |
| O1P | N | ALA- 17 | 3.4 | 152.2 | H-Bond (Protein Donor) |
| O3B | OE1 | GLU- 38 | 2.77 | 164.56 | H-Bond (Ligand Donor) |
| O3B | OE2 | GLU- 38 | 3.09 | 132.59 | H-Bond (Ligand Donor) |
| O2B | OE2 | GLU- 38 | 2.52 | 161.73 | H-Bond (Ligand Donor) |
| N3A | N | ALA- 39 | 3.18 | 141.38 | H-Bond (Protein Donor) |
| O3B | NE2 | HIS- 45 | 2.76 | 149.37 | H-Bond (Protein Donor) |
| C8 | CB | PRO- 47 | 3.98 | 0 | Hydrophobic |
| C9A | SG | CYS- 48 | 3.77 | 0 | Hydrophobic |
| C2' | SG | CYS- 48 | 3.69 | 0 | Hydrophobic |
| C7M | CG | PRO- 51 | 4.26 | 0 | Hydrophobic |
| N6A | O | VAL- 85 | 3.23 | 169.67 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 85 | 3.09 | 159.52 | H-Bond (Protein Donor) |
| C3B | CD2 | LEU- 135 | 3.79 | 0 | Hydrophobic |
| C2B | CD1 | LEU- 135 | 4.01 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 162 | 3.85 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 162 | 3.95 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 283 | 2.63 | 164.7 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 283 | 3.19 | 133.27 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 283 | 4.33 | 0 | Hydrophobic |
| O2P | N | ASP- 283 | 3.01 | 155.2 | H-Bond (Protein Donor) |
| N1 | N | ALA- 301 | 3.35 | 144.29 | H-Bond (Protein Donor) |
| O2 | N | ALA- 301 | 2.92 | 154.32 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 301 | 4.24 | 0 | Hydrophobic |
| N3 | O | TYR- 425 | 2.74 | 175.74 | H-Bond (Ligand Donor) |
| C2' | C2P | COA- 902 | 4.16 | 0 | Hydrophobic |
| C4' | C2P | COA- 902 | 4.08 | 0 | Hydrophobic |
| O2P | O | HOH- 1008 | 2.74 | 159.48 | H-Bond (Protein Donor) |
