sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2014-02-13
| 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: | 26.959 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.099 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.28 | 42.72 |
| According to VolSite | |
| HET Code: | DRN |
|---|---|
| Formula: | C25H24N5O2S |
| Molecular weight: | 458.555 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.94 % |
| Polar Surface area: | 132.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -15.4855 | 8.53006 | -13.9549 |
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 |
| CAC | CB | LEU- 627 | 4.43 | 0 | Hydrophobic |
| SAT | CE2 | PHE- 632 | 3.46 | 0 | Hydrophobic |
| CBE | CE2 | PHE- 632 | 3.9 | 0 | Hydrophobic |
| CAS | CB | PHE- 632 | 3.82 | 0 | Hydrophobic |
| CAB | CB | VAL- 635 | 4.24 | 0 | Hydrophobic |
| CAC | CG1 | VAL- 635 | 3.96 | 0 | Hydrophobic |
| CAP | CG2 | VAL- 635 | 3.83 | 0 | Hydrophobic |
| CAP | CB | LYS- 650 | 4.47 | 0 | Hydrophobic |
| CAQ | CD | LYS- 650 | 3.76 | 0 | Hydrophobic |
| CAP | CG | MET- 701 | 4.43 | 0 | Hydrophobic |
| NAU | O | GLU- 702 | 2.9 | 171.56 | H-Bond (Ligand Donor) |
| OAZ | N | SER- 704 | 3.02 | 177.57 | H-Bond (Protein Donor) |
| NBC | OD2 | ASP- 708 | 2.61 | 161.09 | H-Bond (Ligand Donor) |
| CAY | CB | ASP- 708 | 4.29 | 0 | Hydrophobic |
| NBC | O | ASP- 750 | 2.75 | 145.83 | H-Bond (Ligand Donor) |
| SAT | CB | ASP- 750 | 4.45 | 0 | Hydrophobic |
| CAY | CD2 | LEU- 753 | 4.12 | 0 | Hydrophobic |
| CAE | CD2 | LEU- 753 | 4.45 | 0 | Hydrophobic |
| CA0 | CB | ALA- 763 | 4.03 | 0 | Hydrophobic |
| CAN | CB | ALA- 763 | 4.1 | 0 | Hydrophobic |
| CAS | CB | ASP- 764 | 3.72 | 0 | Hydrophobic |
| CAY | CE1 | PHE- 910 | 3.24 | 0 | Hydrophobic |
