sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-04-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.330 | 5.330 | 5.330 | 0.000 | 5.330 | 1 |
| 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: | 22.213 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.650 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.05 | 58.95 |
| According to VolSite | |
| HET Code: | D1M |
|---|---|
| Formula: | C12H14N2O7 |
| Molecular weight: | 298.249 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.22 % |
| Polar Surface area: | 139.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 34.0871 | 22.8552 | 28.1557 |
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 | 3.16 | 153.86 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 136 | 4.14 | 0 | Hydrophobic |
| C1' | CB | LEU- 136 | 4.28 | 0 | Hydrophobic |
| C6' | CD2 | LEU- 139 | 3.98 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 283 | 2.59 | 171.33 | H-Bond (Ligand Donor) |
| O4 | N | ASN- 284 | 3.04 | 146.37 | H-Bond (Protein Donor) |
| O2' | ND2 | ASN- 284 | 3.1 | 166.3 | H-Bond (Protein Donor) |
| O6' | ND1 | HIS- 377 | 2.77 | 165.82 | H-Bond (Ligand Donor) |
| C7 | CB | HIS- 377 | 3.85 | 0 | Hydrophobic |
| C7 | CB | THR- 378 | 3.91 | 0 | Hydrophobic |
| C8 | CG2 | THR- 378 | 3.47 | 0 | Hydrophobic |
| C8 | CB | ALA- 383 | 4.5 | 0 | Hydrophobic |
| O6' | ND2 | ASN- 484 | 2.77 | 149.14 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 672 | 2.66 | 161.35 | H-Bond (Ligand Donor) |
| O3' | N | SER- 674 | 3 | 179.3 | H-Bond (Protein Donor) |
| C4' | CB | SER- 674 | 4.29 | 0 | Hydrophobic |
| O3' | N | GLY- 675 | 3.07 | 143.69 | H-Bond (Protein Donor) |
| O4' | N | GLY- 675 | 2.77 | 124.88 | H-Bond (Protein Donor) |
| O2' | O | HOH- 1090 | 2.88 | 172.51 | H-Bond (Ligand Donor) |
