sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-12-20
| Name: | Serine/threonine-protein kinase PRP4 homolog |
|---|---|
| ID: | PRP4B_HUMAN |
| AC: | Q13523 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.924 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.210 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.62 | 53.38 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.91 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -2.94545 | -0.304258 | 13.3067 |
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' | CG2 | THR- 693 | 3.54 | 0 | Hydrophobic |
| O2B | N | SER- 699 | 2.87 | 155.01 | H-Bond (Protein Donor) |
| C1' | CG1 | VAL- 701 | 3.84 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 701 | 4.11 | 0 | Hydrophobic |
| O2A | NZ | LYS- 717 | 2.89 | 176.09 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 717 | 2.89 | 0 | Ionic (Protein Cationic) |
| N6 | O | GLU- 768 | 3.03 | 164.1 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 770 | 3.29 | 134.8 | H-Bond (Protein Donor) |
| O3' | ND2 | ASN- 773 | 2.94 | 155.29 | H-Bond (Protein Donor) |
| O3' | O | ASP- 819 | 3.33 | 139.63 | H-Bond (Ligand Donor) |
| C2' | CD1 | LEU- 822 | 3.89 | 0 | Hydrophobic |
| N3B | OD1 | ASP- 834 | 3.12 | 132.71 | H-Bond (Ligand Donor) |
| O2G | MG | MG- 1103 | 2.11 | 0 | Metal Acceptor |
| O1B | MG | MG- 1103 | 1.98 | 0 | Metal Acceptor |
