sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2014-03-25
| Name: | P2Y purinoceptor 12 |
|---|---|
| ID: | P2Y12_HUMAN |
| AC: | Q9H244 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| A | 100 % |
| B-Factor: | 70.707 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.986 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.69 | 43.31 |
| According to VolSite | |
| HET Code: | CLR |
|---|---|
| Formula: | C27H46O |
| Molecular weight: | 386.654 g/mol |
| DrugBank ID: | DB04540 |
| Buried Surface Area: | 42.79 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 5.09432 | -0.984536 | 32.3009 |
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 |
| O1B | CZ | ARG- 93 | 3.83 | 0 | Ionic (Protein Cationic) |
| O1B | NH2 | ARG- 93 | 2.83 | 163.94 | H-Bond (Protein Donor) |
| O3' | O | CYS- 97 | 2.88 | 158.41 | H-Bond (Ligand Donor) |
| C5' | CB | SER- 101 | 4.34 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 102 | 3.97 | 0 | Hydrophobic |
| S1 | CG1 | VAL- 102 | 4.26 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 102 | 3.8 | 0 | Hydrophobic |
| O1A | OH | TYR- 105 | 2.66 | 165.17 | H-Bond (Protein Donor) |
| C1' | CD2 | TYR- 105 | 3.97 | 0 | Hydrophobic |
| S1 | CB | TYR- 105 | 4.38 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 105 | 4.07 | 0 | Hydrophobic |
| S1 | CB | PHE- 106 | 3.82 | 0 | Hydrophobic |
| C11 | CB | LEU- 155 | 3.73 | 0 | Hydrophobic |
| S1 | CB | SER- 156 | 3.68 | 0 | Hydrophobic |
| O2B | N | CYS- 175 | 3 | 162.21 | H-Bond (Protein Donor) |
| C5' | SG | CYS- 175 | 3.75 | 0 | Hydrophobic |
| C3' | CB | CYS- 175 | 4.44 | 0 | Hydrophobic |
| O3' | NZ | LYS- 179 | 2.87 | 160.62 | H-Bond (Protein Donor) |
| O2' | ND1 | HIS- 187 | 2.85 | 161.09 | H-Bond (Protein Donor) |
| C11 | CG1 | VAL- 190 | 3.7 | 0 | Hydrophobic |
| N7 | ND2 | ASN- 191 | 3.29 | 129.98 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 191 | 3.11 | 148 | H-Bond (Ligand Donor) |
| C11 | SG | CYS- 194 | 4.21 | 0 | Hydrophobic |
| O2A | NH2 | ARG- 256 | 2.72 | 168.77 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 256 | 3.66 | 0 | Ionic (Protein Cationic) |
| O3A | NE2 | GLN- 263 | 3.45 | 124.8 | H-Bond (Protein Donor) |
| O2A | NE2 | GLN- 263 | 2.82 | 163.77 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 280 | 2.78 | 168.85 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 280 | 2.78 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 280 | 3.88 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 280 | 2.84 | 0 | Ionic (Protein Cationic) |
| O1B | O | HOH- 1322 | 2.91 | 160.35 | H-Bond (Protein Donor) |
| O2B | O | HOH- 1331 | 2.68 | 152.78 | H-Bond (Protein Donor) |
