sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2011-01-24
| Name: | Cellobiose Phosphorylase |
|---|---|
| ID: | O66264_9CELL |
| AC: | O66264 |
| Organism: | Cellulomonas gilvus |
| Reign: | Bacteria |
| TaxID: | 11 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 5 % |
| B | 95 % |
| B-Factor: | 24.786 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.239 | 786.375 |
| % Hydrophobic | % Polar |
|---|---|
| 29.61 | 70.39 |
| According to VolSite | |
| HET Code: | NOJ |
|---|---|
| Formula: | C6H14NO4 |
| Molecular weight: | 164.180 g/mol |
| DrugBank ID: | DB03206 |
| Buried Surface Area: | 73.19 % |
| Polar Surface area: | 97.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -14.7717 | 74.3683 | 81.4325 |
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 | NH2 | ARG- 362 | 2.76 | 171.84 | H-Bond (Protein Donor) |
| O3 | NH1 | ARG- 367 | 3.11 | 154.89 | H-Bond (Protein Donor) |
| C4 | CD | ARG- 367 | 4.45 | 0 | Hydrophobic |
| O3 | OD1 | ASP- 368 | 2.51 | 172.35 | H-Bond (Ligand Donor) |
| C4 | CE2 | TRP- 488 | 4.35 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 488 | 3.64 | 0 | Hydrophobic |
| O4 | O | TRP- 488 | 2.66 | 162.77 | H-Bond (Ligand Donor) |
| O6 | N | ASP- 490 | 2.65 | 159.61 | H-Bond (Protein Donor) |
| N5 | OE2 | GLU- 659 | 3.34 | 130.99 | H-Bond (Ligand Donor) |
| O6 | OE2 | GLU- 659 | 2.86 | 156.44 | H-Bond (Ligand Donor) |
| N5 | OE2 | GLU- 659 | 3.34 | 0 | Ionic (Ligand Cationic) |
| C6 | CG | GLU- 659 | 4.47 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 664 | 3.76 | 0 | Hydrophobic |
