sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2013-06-22
| Name: | Cytidine and deoxycytidylate deaminase zinc-binding region |
|---|---|
| ID: | Q82Y41_NITEU |
| AC: | Q82Y41 |
| Organism: | Nitrosomonas europaea |
| Reign: | Bacteria |
| TaxID: | 228410 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 18.129 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.779 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.62 | 52.38 |
| According to VolSite | |
| HET Code: | GNG |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.89 % |
| Polar Surface area: | 134.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 23.3581 | 32.1082 | 45.5367 |
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 |
| DuAr | DuAr | PHE- 48 | 3.91 | 0 | Aromatic Face/Face |
| N7 | ND2 | ASN- 66 | 2.92 | 121.02 | H-Bond (Protein Donor) |
| O6 | ND2 | ASN- 66 | 3.25 | 156.36 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 77 | 3.8 | 0 | Aromatic Face/Face |
| O6 | N | ALA- 78 | 2.95 | 174.29 | H-Bond (Protein Donor) |
| N2 | O | GLU- 110 | 3.32 | 175.01 | H-Bond (Ligand Donor) |
| C1' | CB | CYS- 112 | 4.2 | 0 | Hydrophobic |
| C4' | CZ2 | TRP- 121 | 4.05 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 141 | 4.49 | 0 | Hydrophobic |
| C1' | CB | PHE- 141 | 4.46 | 0 | Hydrophobic |
| C3' | CD1 | PHE- 141 | 3.34 | 0 | Hydrophobic |
| O3' | O | ASP- 142 | 2.71 | 122.59 | H-Bond (Ligand Donor) |
| O5' | O | HOH- 314 | 2.96 | 158.1 | H-Bond (Ligand Donor) |
| N3 | O | HOH- 362 | 2.61 | 179.94 | H-Bond (Protein Donor) |
