sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2002-09-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 2 |
| Name: | Cytidine deaminase |
|---|---|
| ID: | CDD_HUMAN |
| AC: | P32320 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.5.4.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 17 % |
| B | 83 % |
| B-Factor: | 32.310 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.615 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.49 | 48.51 |
| According to VolSite | |
| HET Code: | BRD |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB03185 |
| Buried Surface Area: | 72.38 % |
| Polar Surface area: | 102.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 37.4211 | 83.7955 | 119.03 |
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- 34 | 4.34 | 0 | Hydrophobic |
| C4' | CD1 | PHE- 36 | 4.06 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 54 | 2.93 | 170.68 | H-Bond (Protein Donor) |
| C2' | CB | ASN- 54 | 4.31 | 0 | Hydrophobic |
| C3' | CG | GLU- 56 | 4.46 | 0 | Hydrophobic |
| O3' | OE1 | GLU- 56 | 2.82 | 158.58 | H-Bond (Ligand Donor) |
| O5' | O | ALA- 58 | 2.81 | 154.77 | H-Bond (Ligand Donor) |
| C2' | SG | CYS- 59 | 4.35 | 0 | Hydrophobic |
| C3' | CB | TYR- 60 | 4.24 | 0 | Hydrophobic |
| C5' | CD2 | TYR- 60 | 4 | 0 | Hydrophobic |
| O5' | N | TYR- 60 | 3.05 | 155.84 | H-Bond (Protein Donor) |
| C2' | CG | PRO- 61 | 4.21 | 0 | Hydrophobic |
| C2' | SG | CYS- 65 | 4.09 | 0 | Hydrophobic |
| O2 | N | ALA- 66 | 2.92 | 158.16 | H-Bond (Protein Donor) |
| N3 | OE2 | GLU- 67 | 3.46 | 126.29 | H-Bond (Ligand Donor) |
| N3 | OE1 | GLU- 67 | 2.94 | 176.81 | H-Bond (Ligand Donor) |
