sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.040 Å
X-ray
2001-08-21
| Name: | Cytidine deaminase |
|---|---|
| ID: | CDD_BACSU |
| AC: | P19079 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | 3.5.4.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 8.315 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.747 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.65 | 59.35 |
| According to VolSite | |
| HET Code: | THU |
|---|---|
| Formula: | C9H14N2O5 |
| Molecular weight: | 230.218 g/mol |
| DrugBank ID: | DB03562 |
| Buried Surface Area: | 72.86 % |
| Polar Surface area: | 99.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 4.00294 | 64.5909 | 56.1331 |
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 |
| C5' | CB | SER- 22 | 4.13 | 0 | Hydrophobic |
| C4' | CD2 | PHE- 24 | 3.92 | 0 | Hydrophobic |
| C2' | CB | ASN- 42 | 4.1 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 42 | 3.12 | 175.35 | H-Bond (Protein Donor) |
| C3' | CG | GLU- 44 | 4.37 | 0 | Hydrophobic |
| O3' | OE1 | GLU- 44 | 2.62 | 163.89 | H-Bond (Ligand Donor) |
| C3' | CB | CYS- 51 | 4.49 | 0 | Hydrophobic |
| C2' | SG | CYS- 53 | 3.61 | 0 | Hydrophobic |
| O2 | N | ALA- 54 | 3.25 | 160.59 | H-Bond (Protein Donor) |
| N3 | OE1 | GLU- 55 | 2.71 | 156.35 | H-Bond (Ligand Donor) |
| O4 | OE2 | GLU- 55 | 2.58 | 147.08 | H-Bond (Ligand Donor) |
| O4 | N | CYS- 86 | 2.81 | 173.66 | H-Bond (Protein Donor) |
| C5 | CB | CYS- 86 | 4.12 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 125 | 3.87 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 130 | 4.1 | 0 | Hydrophobic |
| O4 | ZN | ZN- 137 | 2.22 | 0 | Metal Acceptor |
