sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2013-03-22
| Name: | E3 ubiquitin-protein ligase Mdm2 |
|---|---|
| ID: | MDM2_XENLA |
| AC: | P56273 |
| Organism: | Xenopus laevis |
| Reign: | Eukaryota |
| TaxID: | 8355 |
| EC Number: | 6.3.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.819 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.188 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 63.86 | 36.14 |
| According to VolSite | |
| HET Code: | 1OY |
|---|---|
| Formula: | C27H31Cl2F2N3O3 |
| Molecular weight: | 554.456 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.16 % |
| Polar Surface area: | 105.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -11.6732 | 19.8462 | 0.00451351 |
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 |
| C35 | CD2 | LEU- 50 | 4.33 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 50 | 3.89 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 50 | 3.91 | 0 | Hydrophobic |
| CL3 | CD1 | LEU- 53 | 3.42 | 0 | Hydrophobic |
| C35 | CB | LEU- 53 | 3.98 | 0 | Hydrophobic |
| CL3 | CD1 | ILE- 57 | 3.94 | 0 | Hydrophobic |
| C44 | CG2 | ILE- 57 | 3.96 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 57 | 3.91 | 0 | Hydrophobic |
| C43 | CG | MET- 58 | 3.76 | 0 | Hydrophobic |
| C44 | CE | MET- 58 | 3.58 | 0 | Hydrophobic |
| C45 | CE2 | TYR- 63 | 3.99 | 0 | Hydrophobic |
| CL3 | CE2 | PHE- 82 | 4.07 | 0 | Hydrophobic |
| CL3 | CZ | PHE- 87 | 4.24 | 0 | Hydrophobic |
| F3 | CG1 | VAL- 89 | 3.24 | 0 | Hydrophobic |
| C14 | CD | LYS- 90 | 4.25 | 0 | Hydrophobic |
| O10 | NE2 | HIS- 92 | 2.72 | 125.64 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 92 | 3.66 | 0 | Aromatic Face/Face |
| CL2 | CB | HIS- 92 | 3.53 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 95 | 4.43 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 95 | 4.21 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 95 | 3.7 | 0 | Hydrophobic |
| CL3 | CG2 | ILE- 95 | 3.72 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 95 | 3.37 | 0 | Hydrophobic |
| CL2 | CE2 | TYR- 96 | 3.48 | 0 | Hydrophobic |
