sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-04-30
| Name: | MccB protein |
|---|---|
| ID: | Q47506_ECOLX |
| AC: | Q47506 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| B | 97 % |
| B-Factor: | 46.965 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.001 | 1245.375 |
| % Hydrophobic | % Polar |
|---|---|
| 34.96 | 65.04 |
| According to VolSite | |
| HET Code: | APC |
|---|---|
| Formula: | C11H14N5O12P3 |
| Molecular weight: | 501.176 g/mol |
| DrugBank ID: | DB02596 |
| Buried Surface Area: | 58.43 % |
| Polar Surface area: | 310.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 3.40945 | 17.2177 | 10.5945 |
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 |
| O1A | N | GLY- 125 | 3.07 | 175.44 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 146 | 2.8 | 162.99 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 146 | 3.18 | 161.34 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 146 | 2.66 | 133.07 | H-Bond (Ligand Donor) |
| O3B | NH2 | ARG- 157 | 2.91 | 135.49 | H-Bond (Protein Donor) |
| O1A | NH2 | ARG- 157 | 2.79 | 122.9 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 157 | 3.59 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 170 | 3.68 | 0 | Ionic (Protein Cationic) |
| O3' | NZ | LYS- 170 | 2.8 | 151.49 | H-Bond (Protein Donor) |
| N6 | O | ILE- 194 | 3.07 | 133.1 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 194 | 2.79 | 171.41 | H-Bond (Protein Donor) |
| N6 | O | HIS- 215 | 2.79 | 157.04 | H-Bond (Ligand Donor) |
| O1A | O | HOH- 382 | 3.07 | 179.94 | H-Bond (Protein Donor) |
