sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2013-08-12
| 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 | 71 % |
| B | 29 % |
| B-Factor: | 43.684 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.420 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 60.45 | 39.55 |
| According to VolSite | |
| HET Code: | T2B |
|---|---|
| Formula: | C15H16I2NO3 |
| Molecular weight: | 512.101 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.43 % |
| Polar Surface area: | 77.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -44.7306 | -3.89705 | 43.7619 |
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 |
| C17 | CE | MET- 40 | 3.38 | 0 | Hydrophobic |
| C1 | SD | MET- 40 | 4.43 | 0 | Hydrophobic |
| C5 | SD | MET- 40 | 4.42 | 0 | Hydrophobic |
| C3 | CE | MET- 40 | 4.11 | 0 | Hydrophobic |
| I3 | CD1 | LEU- 47 | 4.4 | 0 | Hydrophobic |
| I1 | CB | LEU- 47 | 4.32 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 47 | 3.75 | 0 | Hydrophobic |
| O4 | OE2 | GLU- 124 | 3.03 | 166.17 | H-Bond (Ligand Donor) |
| C11 | CD2 | LEU- 126 | 3.97 | 0 | Hydrophobic |
| I3 | CB | LEU- 126 | 4.36 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 128 | 3.98 | 0 | Hydrophobic |
| I3 | CB | PRO- 129 | 3.96 | 0 | Hydrophobic |
| C11 | CB | PRO- 129 | 4.09 | 0 | Hydrophobic |
| C8 | CG | PRO- 129 | 3.89 | 0 | Hydrophobic |
| N1 | OE1 | GLN- 131 | 2.95 | 136.99 | H-Bond (Ligand Donor) |
| I1 | CG | PRO- 234 | 4.2 | 0 | Hydrophobic |
| C6 | CG | PRO- 234 | 3.41 | 0 | Hydrophobic |
| I1 | CB | TYR- 250 | 4.13 | 0 | Hydrophobic |
| C12 | CB | TYR- 250 | 4.12 | 0 | Hydrophobic |
| C12 | CD1 | TYR- 250 | 3.42 | 0 | Hydrophobic |
