sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2013-09-30
| Name: | Receptor-interacting serine/threonine-protein kinase 2 |
|---|---|
| ID: | RIPK2_HUMAN |
| AC: | O43353 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 60.834 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.446 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 61.35 | 38.65 |
| According to VolSite | |
| HET Code: | 0LI |
|---|---|
| Formula: | C29H29F3N6O |
| Molecular weight: | 534.575 g/mol |
| DrugBank ID: | DB08901 |
| Buried Surface Area: | 60.36 % |
| Polar Surface area: | 68.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 14.0185 | 3.69903 | 23.5567 |
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 |
| C11 | CG1 | VAL- 32 | 4.38 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 32 | 4.21 | 0 | Hydrophobic |
| C11 | CB | ALA- 45 | 4.03 | 0 | Hydrophobic |
| C3 | CB | ALA- 45 | 3.86 | 0 | Hydrophobic |
| C11 | CB | LYS- 47 | 3.53 | 0 | Hydrophobic |
| C7 | CD | LYS- 47 | 3.61 | 0 | Hydrophobic |
| N2 | OE2 | GLU- 66 | 2.96 | 134.37 | H-Bond (Ligand Donor) |
| C14 | CG | GLU- 66 | 3.89 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 69 | 4.07 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 69 | 4.08 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 70 | 4.01 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 70 | 3.85 | 0 | Hydrophobic |
| F2 | CD2 | LEU- 70 | 4.02 | 0 | Hydrophobic |
| F1 | CG2 | ILE- 78 | 3.92 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 78 | 3.9 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 79 | 3.42 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 79 | 3.22 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 93 | 4.05 | 0 | Hydrophobic |
| C11 | CG2 | THR- 95 | 3.82 | 0 | Hydrophobic |
| C7 | CG2 | THR- 95 | 3.63 | 0 | Hydrophobic |
| N1 | N | MET- 98 | 2.91 | 166.15 | H-Bond (Protein Donor) |
| F1 | CD2 | LEU- 135 | 4.18 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 142 | 4.12 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 153 | 4.14 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 162 | 4.13 | 0 | Hydrophobic |
| F3 | CG2 | ILE- 162 | 3.78 | 0 | Hydrophobic |
| C10 | CB | ALA- 163 | 4.41 | 0 | Hydrophobic |
| C21 | CB | ASP- 164 | 4.04 | 0 | Hydrophobic |
| F3 | CB | ASP- 164 | 4.17 | 0 | Hydrophobic |
| C18 | CB | ASP- 164 | 3.95 | 0 | Hydrophobic |
| O1 | N | ASP- 164 | 2.66 | 165.46 | H-Bond (Protein Donor) |
| C4 | CE1 | PHE- 165 | 3.84 | 0 | Hydrophobic |
