2.600 Å
X-ray
2012-04-09
| Name: | Glycogen phosphorylase, muscle form |
|---|---|
| ID: | PYGM_RABIT |
| AC: | P00489 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 2.4.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.905 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.082 | 968.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.90 | 56.10 |
| According to VolSite | |

| HET Code: | D1I |
|---|---|
| Formula: | C17H24N2O7 |
| Molecular weight: | 368.382 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.1 % |
| Polar Surface area: | 132.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 34.882 | 23.7785 | 29.2503 |
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 |
| O2 | N | LEU- 136 | 2.94 | 151.58 | H-Bond (Protein Donor) |
| C6' | CD2 | LEU- 139 | 4.2 | 0 | Hydrophobic |
| C13 | CD2 | PHE- 286 | 3.98 | 0 | Hydrophobic |
| O6' | ND1 | HIS- 377 | 2.81 | 170.84 | H-Bond (Ligand Donor) |
| C10 | CB | ALA- 383 | 3.96 | 0 | Hydrophobic |
| O4' | ND2 | ASN- 484 | 3.39 | 129.45 | H-Bond (Protein Donor) |
| O6' | ND2 | ASN- 484 | 2.7 | 151.23 | H-Bond (Protein Donor) |
| O2' | OE1 | GLU- 672 | 2.99 | 159.38 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 672 | 2.73 | 155.48 | H-Bond (Ligand Donor) |
| O3' | N | SER- 674 | 2.92 | 167.08 | H-Bond (Protein Donor) |
| C4' | CB | SER- 674 | 4.34 | 0 | Hydrophobic |
| O3' | N | GLY- 675 | 2.91 | 141.78 | H-Bond (Protein Donor) |
| O4' | N | GLY- 675 | 2.82 | 129.93 | H-Bond (Protein Donor) |
| O2' | O | HOH- 1158 | 2.87 | 144.6 | H-Bond (Protein Donor) |