sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2012-02-01
| Name: | (6-4) photolyase |
|---|---|
| ID: | PHRB_AGRFC |
| AC: | A9CH39 |
| Organism: | Agrobacterium fabrum ) |
| Reign: | Bacteria |
| TaxID: | 176299 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.202 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.783 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 66.67 | 33.33 |
| According to VolSite | |
| HET Code: | DLZ |
|---|---|
| Formula: | C13H18N4O6 |
| Molecular weight: | 326.305 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 78.08 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 13.3087 | 10.9981 | 65.3573 |
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 |
| O2 | N | GLY- 9 | 2.88 | 130.63 | H-Bond (Protein Donor) |
| N1 | N | GLY- 9 | 3.45 | 132.48 | H-Bond (Protein Donor) |
| C4' | CB | ASP- 10 | 4.45 | 0 | Hydrophobic |
| O4' | OD1 | ASP- 10 | 3.4 | 133.62 | H-Bond (Ligand Donor) |
| O5' | OD2 | ASP- 10 | 2.69 | 162.77 | H-Bond (Ligand Donor) |
| O5' | OD1 | ASP- 10 | 3.23 | 133.76 | H-Bond (Ligand Donor) |
| N3 | O | CYS- 32 | 2.83 | 175.52 | H-Bond (Ligand Donor) |
| O4 | N | VAL- 34 | 3.02 | 152.81 | H-Bond (Protein Donor) |
| C2' | CB | GLU- 37 | 4.39 | 0 | Hydrophobic |
| O2' | OE1 | GLU- 37 | 2.7 | 173.12 | H-Bond (Ligand Donor) |
| C6 | CB | ALA- 38 | 4.44 | 0 | Hydrophobic |
| C7 | CE2 | TYR- 40 | 4.46 | 0 | Hydrophobic |
| O3' | OH | TYR- 40 | 3.04 | 140.01 | H-Bond (Ligand Donor) |
| C7 | CD1 | ILE- 51 | 3.42 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 51 | 4.27 | 0 | Hydrophobic |
| O5' | N | GLY- 105 | 2.73 | 146.54 | H-Bond (Protein Donor) |
| C5' | CG | GLU- 106 | 4 | 0 | Hydrophobic |
| C3' | CG2 | VAL- 109 | 4.32 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 109 | 4.41 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 399 | 4.28 | 0 | Hydrophobic |
| C1' | CE1 | TYR- 399 | 4.16 | 0 | Hydrophobic |
| C4' | CD1 | TYR- 399 | 4.39 | 0 | Hydrophobic |
| O2 | O | HOH- 735 | 2.8 | 156.41 | H-Bond (Protein Donor) |
| O5' | O | HOH- 799 | 3.22 | 123.88 | H-Bond (Protein Donor) |
