sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2007-12-19
| Name: | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 |
|---|---|
| ID: | HCN2_MOUSE |
| AC: | O88703 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 14.336 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.764 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 55.14 | 44.86 |
| According to VolSite | |
| HET Code: | CMP |
|---|---|
| Formula: | C10H11N5O6P |
| Molecular weight: | 328.198 g/mol |
| DrugBank ID: | DB02527 |
| Buried Surface Area: | 80.28 % |
| Polar Surface area: | 167.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 53.2875 | 24.6068 | 3.05514 |
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 |
| C5' | CG2 | ILE- 545 | 4.13 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 564 | 4.12 | 0 | Hydrophobic |
| C1' | CB | PHE- 580 | 4.3 | 0 | Hydrophobic |
| O2' | N | GLY- 581 | 2.87 | 155.55 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 582 | 3.07 | 123.71 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 582 | 2.75 | 166.2 | H-Bond (Ligand Donor) |
| C3' | CD1 | ILE- 583 | 3.75 | 0 | Hydrophobic |
| O2P | N | CYS- 584 | 3.04 | 155.52 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 591 | 2.86 | 157.49 | H-Bond (Protein Donor) |
| C5' | CD | ARG- 591 | 4.45 | 0 | Hydrophobic |
| O1P | OG1 | THR- 592 | 2.74 | 166.08 | H-Bond (Protein Donor) |
| O1P | N | THR- 592 | 2.83 | 169.83 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 593 | 4.15 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 595 | 4.24 | 0 | Hydrophobic |
| O2' | NH1 | ARG- 632 | 3.28 | 124.29 | H-Bond (Protein Donor) |
| C2' | CD | ARG- 632 | 4.13 | 0 | Hydrophobic |
