sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-03-26
| 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 | 96 % |
| E | 4 % |
| B-Factor: | 28.026 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.005 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.30 | 45.70 |
| According to VolSite | |
| HET Code: | 1MT |
|---|---|
| Formula: | C25H31Cl2FN4O2 |
| Molecular weight: | 509.444 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.73 % |
| Polar Surface area: | 102.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -14.6774 | 1.33856 | -16.4697 |
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 |
| C23 | CD2 | LEU- 54 | 3.99 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 54 | 3.73 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 54 | 3.64 | 0 | Hydrophobic |
| N2 | O | LEU- 54 | 2.81 | 159.54 | H-Bond (Ligand Donor) |
| CL2 | CD1 | LEU- 57 | 3.7 | 0 | Hydrophobic |
| C23 | CB | LEU- 57 | 3.95 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 61 | 3.71 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 61 | 4.05 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 61 | 3.75 | 0 | Hydrophobic |
| C12 | CG | MET- 62 | 3.24 | 0 | Hydrophobic |
| C14 | SD | MET- 62 | 4.44 | 0 | Hydrophobic |
| C13 | CG | TYR- 67 | 3.91 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 67 | 3.51 | 0 | Hydrophobic |
| C11 | CD1 | TYR- 67 | 4.31 | 0 | Hydrophobic |
| CL2 | CZ | PHE- 86 | 3.75 | 0 | Hydrophobic |
| CL2 | CZ | PHE- 91 | 4.19 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 93 | 4.03 | 0 | Hydrophobic |
| CL1 | CB | HIS- 96 | 3.83 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 96 | 2.64 | 145.05 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 96 | 3.92 | 0 | Aromatic Face/Face |
| CL1 | CG2 | ILE- 99 | 3.85 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 99 | 4.47 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 99 | 4.1 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 99 | 3.56 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 99 | 4.09 | 0 | Hydrophobic |
| CL1 | CE2 | TYR- 100 | 3.65 | 0 | Hydrophobic |
| CL2 | CD1 | ILE- 103 | 4.22 | 0 | Hydrophobic |
