sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2014-02-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.700 | 6.720 | 6.700 | 0.030 | 6.770 | 3 |
| Name: | Serine/threonine-protein kinase N1 |
|---|---|
| ID: | PKN1_HUMAN |
| AC: | Q16512 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.362 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.114 | 975.375 |
| % Hydrophobic | % Polar |
|---|---|
| 49.83 | 50.17 |
| According to VolSite | |
| HET Code: | MI1 |
|---|---|
| Formula: | C16H20N6O |
| Molecular weight: | 312.370 g/mol |
| DrugBank ID: | DB08895 |
| Buried Surface Area: | 68.49 % |
| Polar Surface area: | 88.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -14.9529 | 8.89339 | -12.741 |
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 |
| C9 | CB | LEU- 627 | 3.93 | 0 | Hydrophobic |
| N24 | N | GLY- 630 | 3.29 | 120.29 | H-Bond (Protein Donor) |
| C1 | CG2 | VAL- 635 | 4.14 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 635 | 4.37 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 635 | 4.13 | 0 | Hydrophobic |
| C15 | CB | ALA- 648 | 4.17 | 0 | Hydrophobic |
| N12 | O | GLU- 702 | 2.94 | 172.62 | H-Bond (Ligand Donor) |
| N17 | N | SER- 704 | 3.1 | 171.95 | H-Bond (Protein Donor) |
| C15 | CD1 | LEU- 753 | 3.58 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 753 | 3.47 | 0 | Hydrophobic |
| C5 | CB | ALA- 763 | 3.89 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 910 | 3.88 | 0 | Hydrophobic |
