sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-06-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.160 | 5.310 | 5.390 | 0.110 | 5.390 | 3 |
| Name: | Aminopeptidase N |
|---|---|
| ID: | AMPN_PIG |
| AC: | P15145 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | 3.4.11.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.042 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.452 | 766.125 |
| % Hydrophobic | % Polar |
|---|---|
| 28.19 | 71.81 |
| According to VolSite | |
| HET Code: | BES |
|---|---|
| Formula: | C16H24N2O4 |
| Molecular weight: | 308.373 g/mol |
| DrugBank ID: | DB03424 |
| Buried Surface Area: | 53.21 % |
| Polar Surface area: | 117.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 27.7327 | 16.8185 | 58.6016 |
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 |
| N2 | OE1 | GLN- 208 | 2.82 | 156.2 | H-Bond (Ligand Donor) |
| C12 | CB | GLN- 208 | 3.94 | 0 | Hydrophobic |
| N1 | O | ALA- 348 | 3.12 | 141.07 | H-Bond (Ligand Donor) |
| C6 | SD | MET- 349 | 3.35 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 350 | 2.67 | 176.28 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 350 | 3.43 | 126.38 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 350 | 2.67 | 0 | Ionic (Ligand Cationic) |
| N2 | OE2 | GLU- 350 | 3.43 | 0 | Ionic (Ligand Cationic) |
| C15 | CG2 | VAL- 380 | 4.49 | 0 | Hydrophobic |
| C15 | CB | HIS- 383 | 3.79 | 0 | Hydrophobic |
| O2 | OE2 | GLU- 384 | 2.74 | 160 | H-Bond (Ligand Donor) |
| O2 | OE1 | GLU- 384 | 3.35 | 140.44 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 406 | 2.77 | 170.55 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 406 | 2.77 | 0 | Ionic (Ligand Cationic) |
| O3 | OH | TYR- 472 | 3 | 147.85 | H-Bond (Protein Donor) |
| C16 | CE2 | TYR- 472 | 3.88 | 0 | Hydrophobic |
| O2 | ZN | ZN- 1025 | 2.2 | 0 | Metal Acceptor |
