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
1999-09-20
| Name: | Maltodextrin phosphorylase |
|---|---|
| ID: | PHSM_ECOLI |
| AC: | P00490 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.4.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.264 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.070 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.24 | 56.76 |
| According to VolSite | |
| HET Code: | PLP |
|---|---|
| Formula: | C8H8NO6P |
| Molecular weight: | 245.126 g/mol |
| DrugBank ID: | DB00114 |
| Buried Surface Area: | 70.53 % |
| Polar Surface area: | 132.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 10.4944 | 28.0047 | 21.6915 |
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 |
| C2A | CD2 | LEU- 69 | 3.78 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 69 | 4.5 | 0 | Hydrophobic |
| C3 | CG | ARG- 117 | 4.08 | 0 | Hydrophobic |
| O3P | NZ | LYS- 533 | 2.58 | 0 | Ionic (Protein Cationic) |
| O1P | NZ | LYS- 539 | 3.07 | 142.91 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 539 | 3.07 | 0 | Ionic (Protein Cationic) |
| C2A | CE2 | TYR- 613 | 3.68 | 0 | Hydrophobic |
| C2A | CG2 | VAL- 615 | 4.17 | 0 | Hydrophobic |
| C2A | CB | ALA- 618 | 4.23 | 0 | Hydrophobic |
| O2P | N | THR- 641 | 2.65 | 157.83 | H-Bond (Protein Donor) |
| O2P | N | GLY- 642 | 3.17 | 175.53 | H-Bond (Protein Donor) |
| C4A | CE | LYS- 645 | 3.38 | 0 | Hydrophobic |
| O3P | O | HOH- 2295 | 2.94 | 136.25 | H-Bond (Protein Donor) |
