sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-03-21
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 33.431 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.275 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 72.41 | 27.59 |
| According to VolSite | |
| HET Code: | I09 |
|---|---|
| Formula: | C27H33Cl2N3O3 |
| Molecular weight: | 518.475 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.94 % |
| 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 |
|---|---|---|
| 4.88506 | -29.2287 | 15.9681 |
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 |
| CL2 | CD2 | LEU- 50 | 3.67 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 50 | 3.46 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 50 | 3.8 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 50 | 3.85 | 0 | Hydrophobic |
| CL3 | CB | LEU- 53 | 3.89 | 0 | Hydrophobic |
| C35 | CB | LEU- 53 | 3.89 | 0 | Hydrophobic |
| CL3 | CD1 | ILE- 57 | 3.75 | 0 | Hydrophobic |
| C44 | CG2 | ILE- 57 | 4.11 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 57 | 3.71 | 0 | Hydrophobic |
| C44 | SD | MET- 58 | 4.29 | 0 | Hydrophobic |
| C43 | CG | MET- 58 | 3.52 | 0 | Hydrophobic |
| CL3 | CE2 | PHE- 82 | 3.87 | 0 | Hydrophobic |
| CL3 | CZ | PHE- 87 | 4.08 | 0 | Hydrophobic |
| C32 | CB | VAL- 89 | 3.68 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 89 | 4.26 | 0 | Hydrophobic |
| C4 | CB | VAL- 89 | 4.36 | 0 | Hydrophobic |
| C44 | CG1 | VAL- 89 | 4.25 | 0 | Hydrophobic |
| C14 | CG | LYS- 90 | 3.84 | 0 | Hydrophobic |
| O10 | NE2 | HIS- 92 | 2.7 | 162.7 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 92 | 3.66 | 0 | Aromatic Face/Face |
| CL2 | CB | HIS- 92 | 3.71 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 95 | 4.17 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 95 | 3.84 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 95 | 3.74 | 0 | Hydrophobic |
| CL3 | CG2 | ILE- 95 | 4.1 | 0 | Hydrophobic |
| CL2 | CE2 | TYR- 96 | 3.79 | 0 | Hydrophobic |
