sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2010-01-29
| Name: | Agglutinin alpha chain |
|---|---|
| ID: | LECA_MACPO |
| AC: | P18674 |
| Organism: | Maclura pomifera |
| Reign: | Eukaryota |
| TaxID: | 3496 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 56 % |
| C | 30 % |
| G | 11 % |
| H | 4 % |
| B-Factor: | 19.643 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.477 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.87 | 55.13 |
| According to VolSite | |
| HET Code: | LEC |
|---|---|
| Formula: | C14H18N2O8 |
| Molecular weight: | 342.301 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.07 % |
| Polar Surface area: | 154.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 25.4193 | 129.739 | 15.9047 |
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 |
| O3 | N | GLY- 1 | 2.96 | 140.21 | H-Bond (Protein Donor) |
| O4 | N | GLY- 1 | 2.99 | 134.76 | H-Bond (Protein Donor) |
| O1' | CZ | ARG- 13 | 3.32 | 0 | Ionic (Protein Cationic) |
| C1 | CE1 | PHE- 47 | 4.3 | 0 | Hydrophobic |
| C3' | CG | PRO- 61 | 4.11 | 0 | Hydrophobic |
| C5' | CG | PRO- 61 | 4.19 | 0 | Hydrophobic |
| C5' | CB | GLU- 76 | 4.41 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 78 | 3.56 | 0 | Hydrophobic |
| C6 | CB | TYR- 78 | 3.98 | 0 | Hydrophobic |
| C6' | CE1 | TYR- 78 | 3.37 | 0 | Hydrophobic |
| C4 | CD2 | TYR- 78 | 3.69 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 80 | 3.73 | 0 | Hydrophobic |
| C6 | CB | TYR- 122 | 4.38 | 0 | Hydrophobic |
| C1 | CD1 | TYR- 122 | 3.96 | 0 | Hydrophobic |
| C6' | CB | TYR- 122 | 4.06 | 0 | Hydrophobic |
| O5 | N | TYR- 122 | 3.1 | 167.78 | H-Bond (Protein Donor) |
| DuAr | DuAr | TYR- 122 | 3.69 | 0 | Aromatic Face/Face |
| C6 | CE3 | TRP- 123 | 3.77 | 0 | Hydrophobic |
| O6 | N | TRP- 123 | 2.89 | 167.41 | H-Bond (Protein Donor) |
| O4 | OD1 | ASP- 125 | 2.6 | 163.51 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 125 | 3.12 | 126.7 | H-Bond (Ligand Donor) |
| O6 | OD1 | ASP- 125 | 2.78 | 151.82 | H-Bond (Ligand Donor) |
