sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2006-06-30
| Name: | Elongation factor 3A |
|---|---|
| ID: | EF3A_YEAST |
| AC: | P16521 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 25.284 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.557 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.18 | 61.82 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.24 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 263.092 | -77.5914 | 116.506 |
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 | NE2 | HIS- 43 | 3.05 | 168.58 | H-Bond (Protein Donor) |
| N7 | N | HIS- 43 | 2.75 | 165.28 | H-Bond (Protein Donor) |
| N6 | O | ASP- 44 | 3.19 | 136.51 | H-Bond (Ligand Donor) |
| N1 | OG | SER- 82 | 2.97 | 157.53 | H-Bond (Protein Donor) |
| C4' | CB | THR- 391 | 4.09 | 0 | Hydrophobic |
| C1' | CB | THR- 391 | 3.69 | 0 | Hydrophobic |
| N3 | OG1 | THR- 391 | 3.16 | 163.44 | H-Bond (Protein Donor) |
| O2A | ND1 | HIS- 395 | 2.82 | 135.45 | H-Bond (Protein Donor) |
| O5' | N | GLU- 396 | 3.45 | 155.79 | H-Bond (Protein Donor) |
| C4' | CB | GLU- 396 | 4.12 | 0 | Hydrophobic |
| C3' | CB | ASN- 924 | 4.32 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 924 | 3.27 | 163.7 | H-Bond (Ligand Donor) |
| N3B | O | HIS- 950 | 3.17 | 133.28 | H-Bond (Ligand Donor) |
| C5' | CB | HIS- 950 | 3.97 | 0 | Hydrophobic |
