sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.250 Å
X-ray
2013-02-13
| 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: | 10.674 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.316 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 65.74 | 34.26 |
| According to VolSite | |
| HET Code: | I31 |
|---|---|
| Formula: | C29H33Cl2N2O |
| Molecular weight: | 496.491 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.46 % |
| Polar Surface area: | 35.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -3.7965 | 3.92382 | 1.09462 |
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 |
| C53 | CD2 | LEU- 50 | 3.92 | 0 | Hydrophobic |
| C43 | CD1 | LEU- 50 | 3.65 | 0 | Hydrophobic |
| C44 | CD2 | LEU- 50 | 3.83 | 0 | Hydrophobic |
| C53 | CB | LEU- 53 | 3.86 | 0 | Hydrophobic |
| CL5 | CD1 | ILE- 57 | 3.84 | 0 | Hydrophobic |
| C29 | CG2 | ILE- 57 | 3.72 | 0 | Hydrophobic |
| C55 | CD1 | ILE- 57 | 3.76 | 0 | Hydrophobic |
| C29 | SD | MET- 58 | 3.64 | 0 | Hydrophobic |
| C31 | CB | GLN- 68 | 3.82 | 0 | Hydrophobic |
| C32 | CB | HIS- 69 | 3.61 | 0 | Hydrophobic |
| CL5 | CE1 | PHE- 82 | 3.94 | 0 | Hydrophobic |
| CL5 | CE1 | PHE- 87 | 3.89 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 89 | 4.47 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 89 | 4.12 | 0 | Hydrophobic |
| C55 | CG1 | VAL- 89 | 3.83 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 89 | 3.78 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 92 | 3.89 | 0 | Aromatic Face/Face |
| CL4 | CB | HIS- 92 | 3.74 | 0 | Hydrophobic |
| CL5 | CG2 | ILE- 95 | 4.04 | 0 | Hydrophobic |
| CL4 | CG2 | ILE- 95 | 3.84 | 0 | Hydrophobic |
| C45 | CD1 | ILE- 95 | 3.75 | 0 | Hydrophobic |
| CL4 | CE1 | TYR- 96 | 3.49 | 0 | Hydrophobic |
| N3 | O | HOH- 309 | 2.8 | 173.06 | H-Bond (Ligand Donor) |
