sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.580 Å
X-ray
2012-07-06
| Name: | Glycylpeptide N-tetradecanoyltransferase |
|---|---|
| ID: | A5K1A2_PLAVS |
| AC: | A5K1A2 |
| Organism: | Plasmodium vivax |
| Reign: | Eukaryota |
| TaxID: | 126793 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.697 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.778 | 1721.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.10 | 44.90 |
| According to VolSite | |
| HET Code: | X25 |
|---|---|
| Formula: | C23H24N3O3 |
| Molecular weight: | 390.455 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.97 % |
| Polar Surface area: | 77.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 24.1921 | 42.8708 | 63.8872 |
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 |
| C22 | CG1 | VAL- 96 | 3.57 | 0 | Hydrophobic |
| C22 | CB | ASP- 98 | 3.94 | 0 | Hydrophobic |
| C17 | CB | ASP- 98 | 3.59 | 0 | Hydrophobic |
| C19 | CB | PHE- 103 | 3.63 | 0 | Hydrophobic |
| C | CZ | PHE- 105 | 3.2 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 105 | 4.05 | 0 | Hydrophobic |
| C20 | CD1 | PHE- 105 | 3.35 | 0 | Hydrophobic |
| C13 | CB | TYR- 211 | 4.24 | 0 | Hydrophobic |
| C | CE2 | TYR- 211 | 4.22 | 0 | Hydrophobic |
| C4 | CB | TYR- 211 | 3.27 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 211 | 3.97 | 0 | Aromatic Face/Face |
| C12 | CD2 | LEU- 317 | 3.59 | 0 | Hydrophobic |
| C19 | CB | SER- 319 | 4.43 | 0 | Hydrophobic |
| C8 | CD2 | TYR- 334 | 4.45 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 334 | 4.43 | 0 | Hydrophobic |
| C5 | CD2 | TYR- 334 | 3.4 | 0 | Hydrophobic |
| C4 | CB | ASN- 365 | 3.52 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 367 | 4.31 | 0 | Hydrophobic |
| C6 | CG | LEU- 367 | 3.78 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 388 | 3.88 | 0 | Hydrophobic |
| N | OXT | LEU- 410 | 3.68 | 0 | Ionic (Ligand Cationic) |
| N | O | LEU- 410 | 2.86 | 0 | Ionic (Ligand Cationic) |
| N | O | LEU- 410 | 2.86 | 160.35 | H-Bond (Ligand Donor) |
| N2 | O | HOH- 2250 | 3.42 | 179.99 | H-Bond (Protein Donor) |
