sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2012-10-02
| 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: | 36.939 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.819 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 80.33 | 19.67 |
| According to VolSite | |
| HET Code: | 13Q |
|---|---|
| Formula: | C23H22Cl2NO3 |
| Molecular weight: | 431.332 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.39 % |
| Polar Surface area: | 60.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 9.07231 | 3.02241 | 2.36331 |
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 |
| C5 | CG1 | VAL- 14 | 4.34 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 14 | 3.26 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 14 | 3.41 | 0 | Hydrophobic |
| C17 | CB | THR- 16 | 4.47 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 54 | 4.03 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 54 | 3.3 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 54 | 3.69 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 57 | 4.02 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 61 | 3.65 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 61 | 3.45 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 61 | 3.8 | 0 | Hydrophobic |
| C20 | SD | MET- 62 | 4.45 | 0 | Hydrophobic |
| C20 | CE1 | TYR- 67 | 3.65 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 93 | 4.29 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 93 | 3.71 | 0 | Hydrophobic |
| O2 | NE2 | HIS- 96 | 3.1 | 130.64 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 96 | 3.65 | 0 | Aromatic Face/Face |
| CL2 | CB | HIS- 96 | 3.82 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 99 | 4.45 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 99 | 4.31 | 0 | Hydrophobic |
| CL2 | CB | ILE- 99 | 4.22 | 0 | Hydrophobic |
| CL2 | CD2 | TYR- 100 | 4.08 | 0 | Hydrophobic |
