sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2011-12-05
| Name: | NADPH-dependent 7-cyano-7-deazaguanine reductase |
|---|---|
| ID: | QUEF_VIBCH |
| AC: | Q9KTK0 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 243277 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 48 % |
| D | 52 % |
| B-Factor: | 13.574 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.966 | 857.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 54.68 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 21.7717 | 19.2625 | -7.35669 |
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 |
| N1A | OG | SER- 95 | 2.76 | 163.85 | H-Bond (Protein Donor) |
| O4B | NZ | LYS- 96 | 3.45 | 127.8 | H-Bond (Protein Donor) |
| O2N | NZ | LYS- 96 | 3.4 | 165.01 | H-Bond (Protein Donor) |
| O2N | NZ | LYS- 96 | 3.4 | 0 | Ionic (Protein Cationic) |
| C4D | CD | LYS- 96 | 4.27 | 0 | Hydrophobic |
| C1D | CB | LYS- 96 | 3.49 | 0 | Hydrophobic |
| C1B | CD | LYS- 99 | 3.64 | 0 | Hydrophobic |
| C4B | CE | LYS- 99 | 3.79 | 0 | Hydrophobic |
| C2D | CD | LYS- 99 | 3.8 | 0 | Hydrophobic |
| N6A | OG1 | THR- 197 | 2.91 | 166.54 | H-Bond (Ligand Donor) |
| N7A | NE2 | GLN- 199 | 3.23 | 147.68 | H-Bond (Protein Donor) |
| C4B | CG | GLN- 199 | 4.08 | 0 | Hydrophobic |
| C1D | CB | LEU- 262 | 4.36 | 0 | Hydrophobic |
| O2X | N | GLY- 263 | 2.93 | 173.3 | H-Bond (Protein Donor) |
| O3X | N | GLY- 263 | 2.76 | 153.96 | H-Bond (Protein Donor) |
