sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2011-11-26
| Name: | Proliferating cell nuclear antigen |
|---|---|
| ID: | PCNA_HUMAN |
| AC: | P12004 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.017 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.636 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 54.29 | 45.71 |
| According to VolSite | |
| HET Code: | T3 |
|---|---|
| Formula: | C15H12I3NO4 |
| Molecular weight: | 650.973 g/mol |
| DrugBank ID: | DB00279 |
| Buried Surface Area: | 46.07 % |
| Polar Surface area: | 97.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -18.8357 | 3.01865 | 37.3505 |
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 |
| C1 | SD | MET- 40 | 4.04 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 47 | 4.28 | 0 | Hydrophobic |
| C5 | CB | LEU- 47 | 4.22 | 0 | Hydrophobic |
| I1 | CB | LEU- 47 | 4.31 | 0 | Hydrophobic |
| I3 | CD1 | LEU- 47 | 3.81 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 47 | 3.61 | 0 | Hydrophobic |
| I3 | CB | LEU- 126 | 4.3 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 128 | 4.03 | 0 | Hydrophobic |
| I2 | CG | PRO- 129 | 3.99 | 0 | Hydrophobic |
| C8 | CG | PRO- 129 | 3.73 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 131 | 3.08 | 155.76 | H-Bond (Protein Donor) |
| I1 | CG | PRO- 234 | 4.17 | 0 | Hydrophobic |
| I2 | CG | PRO- 234 | 4.32 | 0 | Hydrophobic |
| C6 | CG | PRO- 234 | 3.53 | 0 | Hydrophobic |
| I1 | CB | TYR- 250 | 4.02 | 0 | Hydrophobic |
| C12 | CD1 | TYR- 250 | 3.35 | 0 | Hydrophobic |
| C12 | CB | TYR- 250 | 3.86 | 0 | Hydrophobic |
