sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-04-20
| Name: | E3 ubiquitin-protein ligase Mdm2 |
|---|---|
| ID: | MDM2_HUMAN |
| AC: | Q00987 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 6.3.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.737 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.240 | 290.250 |
| % Hydrophobic | % Polar |
|---|---|
| 60.47 | 39.53 |
| According to VolSite | |
| HET Code: | 0R2 |
|---|---|
| Formula: | C27H30Cl2NO5 |
| Molecular weight: | 519.437 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.79 % |
| Polar Surface area: | 86.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 11.7347 | 26.2761 | 19.2131 |
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 |
| C4 | CD2 | LEU- 54 | 4.12 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 54 | 3.64 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 54 | 3.75 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 55 | 3.96 | 0 | Hydrophobic |
| C26 | CD1 | PHE- 55 | 3.72 | 0 | Hydrophobic |
| C4 | CB | LEU- 57 | 4.06 | 0 | Hydrophobic |
| CL1 | CB | LEU- 57 | 4.02 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 61 | 4.06 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 61 | 3.67 | 0 | Hydrophobic |
| C10 | CE | MET- 62 | 4.13 | 0 | Hydrophobic |
| C25 | SD | MET- 62 | 4.46 | 0 | Hydrophobic |
| C23 | CZ | TYR- 67 | 3.85 | 0 | Hydrophobic |
| CL1 | CE2 | PHE- 86 | 3.92 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 91 | 4.08 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 93 | 3.69 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 93 | 3.84 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 93 | 4.05 | 0 | Hydrophobic |
| O2 | NZ | LYS- 94 | 3.3 | 0 | Ionic (Protein Cationic) |
| O3 | NZ | LYS- 94 | 2.66 | 0 | Ionic (Protein Cationic) |
| O3 | NZ | LYS- 94 | 2.66 | 148.89 | H-Bond (Protein Donor) |
| O2 | NE2 | HIS- 96 | 2.94 | 157.41 | H-Bond (Protein Donor) |
| CL2 | CB | HIS- 96 | 3.68 | 0 | Hydrophobic |
| C21 | CB | HIS- 96 | 3.9 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 96 | 3.71 | 0 | Aromatic Face/Face |
| CL2 | CG2 | ILE- 99 | 3.58 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 99 | 4.4 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 99 | 3.86 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 99 | 3.73 | 0 | Hydrophobic |
| CL2 | CD2 | TYR- 100 | 3.99 | 0 | Hydrophobic |
