sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2003-12-12
| 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 | 25 % |
| C | 75 % |
| B-Factor: | 53.107 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.438 | 2082.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.51 | 41.49 |
| According to VolSite | |
| HET Code: | IMZ |
|---|---|
| Formula: | C31H36Br2N4O4 |
| Molecular weight: | 688.450 g/mol |
| DrugBank ID: | DB02872 |
| Buried Surface Area: | 58.35 % |
| Polar Surface area: | 80.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 14.9593 | 12.6682 | 11.8792 |
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 |
| C41 | CB | LEU- 54 | 4.41 | 0 | Hydrophobic |
| C42 | CD1 | LEU- 54 | 3.68 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 54 | 3.22 | 0 | Hydrophobic |
| C55 | CB | LEU- 54 | 4.39 | 0 | Hydrophobic |
| C54 | CD2 | LEU- 54 | 4.37 | 0 | Hydrophobic |
| C43 | CD2 | LEU- 54 | 4.11 | 0 | Hydrophobic |
| BR53 | CB | LEU- 57 | 3.94 | 0 | Hydrophobic |
| C54 | CB | LEU- 57 | 3.87 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 61 | 3.8 | 0 | Hydrophobic |
| BR53 | CD1 | ILE- 61 | 3.77 | 0 | Hydrophobic |
| C52 | CD1 | ILE- 61 | 4.04 | 0 | Hydrophobic |
| C27 | SD | MET- 62 | 3.54 | 0 | Hydrophobic |
| C28 | CG | MET- 62 | 3.45 | 0 | Hydrophobic |
| C25 | CB | GLN- 72 | 4.47 | 0 | Hydrophobic |
| C24 | CB | GLN- 72 | 4.47 | 0 | Hydrophobic |
| C23 | CB | HIS- 73 | 4.27 | 0 | Hydrophobic |
| C24 | CB | HIS- 73 | 4.4 | 0 | Hydrophobic |
| BR53 | CZ | PHE- 91 | 4.23 | 0 | Hydrophobic |
| C45 | CB | VAL- 93 | 4.36 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 93 | 3.86 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 93 | 4.39 | 0 | Hydrophobic |
| C51 | CG1 | VAL- 93 | 3.77 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 93 | 3.96 | 0 | Hydrophobic |
| BR43 | CB | HIS- 96 | 4.37 | 0 | Hydrophobic |
| C24 | CB | HIS- 96 | 4.25 | 0 | Hydrophobic |
| C44 | CD1 | ILE- 99 | 4.03 | 0 | Hydrophobic |
| BR43 | CG2 | ILE- 99 | 4.14 | 0 | Hydrophobic |
| BR53 | CG2 | ILE- 99 | 4.06 | 0 | Hydrophobic |
| BR43 | CE1 | TYR- 100 | 3.94 | 0 | Hydrophobic |
| C24 | CE1 | TYR- 100 | 4.2 | 0 | Hydrophobic |
| O17 | OH | TYR- 100 | 3.46 | 159.04 | H-Bond (Protein Donor) |
