sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.590 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 |
|---|---|
| C | 100 % |
| B-Factor: | 17.471 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.052 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.99 | 42.01 |
| According to VolSite | |
| HET Code: | 7I1 |
|---|---|
| Formula: | C26H27N2O3 |
| Molecular weight: | 415.504 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.96 % |
| Polar Surface area: | 68.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 3.25313 | -9.93777 | 88.3598 |
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 |
| C23 | CG1 | VAL- 96 | 3.66 | 0 | Hydrophobic |
| C16 | CB | ASP- 98 | 3.9 | 0 | Hydrophobic |
| C20 | CB | ASP- 98 | 4.02 | 0 | Hydrophobic |
| C24 | CB | ASP- 98 | 3.63 | 0 | Hydrophobic |
| C19 | CB | PHE- 103 | 3.55 | 0 | Hydrophobic |
| C | CZ | PHE- 105 | 3.75 | 0 | Hydrophobic |
| C22 | CE1 | PHE- 105 | 3.47 | 0 | Hydrophobic |
| N | OH | TYR- 107 | 3.15 | 132.29 | H-Bond (Ligand Donor) |
| C4 | CB | TYR- 211 | 3.43 | 0 | Hydrophobic |
| C12 | CZ | TYR- 315 | 4.43 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 317 | 4.45 | 0 | Hydrophobic |
| C21 | CB | SER- 319 | 4.35 | 0 | Hydrophobic |
| C19 | CB | SER- 319 | 4.41 | 0 | Hydrophobic |
| C12 | CD2 | TYR- 334 | 4.22 | 0 | Hydrophobic |
| C4 | CB | ASN- 365 | 4.09 | 0 | Hydrophobic |
| C6 | CG | LEU- 367 | 3.94 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 367 | 3.88 | 0 | Hydrophobic |
| C | CD1 | LEU- 388 | 4.34 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 388 | 4.44 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 388 | 3.82 | 0 | Hydrophobic |
| N | OXT | LEU- 410 | 3.47 | 138.17 | H-Bond (Ligand Donor) |
| N | O | LEU- 410 | 3.12 | 133.4 | H-Bond (Ligand Donor) |
| N | OXT | LEU- 410 | 3.47 | 0 | Ionic (Ligand Cationic) |
| N | O | LEU- 410 | 3.12 | 0 | Ionic (Ligand Cationic) |
