sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.000 Å
X-ray
2006-03-23
| Name: | Methionine aminopeptidase |
|---|---|
| ID: | MAP1_ECOLI |
| AC: | P0AE18 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 11.969 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.550 | 347.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.43 | 47.57 |
| According to VolSite | |
| HET Code: | U12 |
|---|---|
| Formula: | C10H9F3N6 |
| Molecular weight: | 270.214 g/mol |
| DrugBank ID: | DB08666 |
| Buried Surface Area: | 64.72 % |
| Polar Surface area: | 102.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.878 | -0.540526 | 9.13432 |
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 |
| C6 | SG | CYS- 59 | 4.01 | 0 | Hydrophobic |
| F2 | CE2 | TYR- 62 | 3.73 | 0 | Hydrophobic |
| F2 | CB | HIS- 63 | 3.82 | 0 | Hydrophobic |
| C9 | CB | TYR- 65 | 3.78 | 0 | Hydrophobic |
| C6 | SG | CYS- 70 | 3.78 | 0 | Hydrophobic |
| N5 | OD1 | ASP- 97 | 3.29 | 138.88 | H-Bond (Ligand Donor) |
| N1 | NE2 | HIS- 171 | 3.32 | 120.04 | H-Bond (Ligand Donor) |
| N2 | NE2 | HIS- 171 | 3.46 | 124.17 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 204 | 3.2 | 144.54 | H-Bond (Ligand Donor) |
| C5 | CZ3 | TRP- 221 | 3.46 | 0 | Hydrophobic |
| F1 | CZ3 | TRP- 221 | 3.42 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 235 | 3.39 | 142.36 | H-Bond (Ligand Donor) |
