sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.840 Å
X-ray
2012-11-12
| Name: | E3 ubiquitin-protein ligase XIAP |
|---|---|
| ID: | XIAP_HUMAN |
| AC: | P98170 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 6.3.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 19 % |
| D | 69 % |
| E | 12 % |
| B-Factor: | 81.197 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.953 | 1549.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.38 | 63.62 |
| According to VolSite | |
| HET Code: | 1AQ |
|---|---|
| Formula: | C31H47F2N5O5 |
| Molecular weight: | 607.732 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.77 % |
| Polar Surface area: | 118.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -5.87005 | 7.69614 | -5.30988 |
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 |
| C26 | CD1 | LEU- 292 | 3.93 | 0 | Hydrophobic |
| C28 | CD | LYS- 297 | 4.43 | 0 | Hydrophobic |
| C27 | CB | LYS- 297 | 3.75 | 0 | Hydrophobic |
| C26 | CG | LYS- 299 | 4.36 | 0 | Hydrophobic |
| N18 | O | GLY- 306 | 3.05 | 152.9 | H-Bond (Ligand Donor) |
| C39 | CB | LEU- 307 | 4.41 | 0 | Hydrophobic |
| O31 | N | THR- 308 | 3.02 | 151.41 | H-Bond (Protein Donor) |
| N34 | O | THR- 308 | 2.79 | 169.4 | H-Bond (Ligand Donor) |
| C28 | CB | THR- 308 | 4.02 | 0 | Hydrophobic |
| C44 | CG2 | THR- 308 | 4.17 | 0 | Hydrophobic |
| C42 | CB | ASP- 309 | 4.48 | 0 | Hydrophobic |
| C48 | CB | ASP- 309 | 3.76 | 0 | Hydrophobic |
| F46 | CB | ASP- 309 | 3.65 | 0 | Hydrophobic |
| C39 | CD2 | TRP- 310 | 3.91 | 0 | Hydrophobic |
| N40 | OE2 | GLU- 314 | 2.92 | 0 | Ionic (Ligand Cationic) |
| N40 | OE1 | GLU- 314 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N40 | OE1 | GLU- 314 | 2.76 | 154.03 | H-Bond (Ligand Donor) |
| C39 | CG | GLN- 319 | 4.09 | 0 | Hydrophobic |
| O36 | NE1 | TRP- 323 | 3.29 | 137.19 | H-Bond (Protein Donor) |
| C4 | CE3 | TRP- 323 | 4.19 | 0 | Hydrophobic |
| C6 | CZ3 | TRP- 323 | 3.42 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 344 | 4.48 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 344 | 4.13 | 0 | Hydrophobic |
| C21 | CG2 | THR- 345 | 3.52 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 348 | 4.07 | 0 | Hydrophobic |
| C22 | CG | GLU- 349 | 4.48 | 0 | Hydrophobic |
