sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-04-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.400 | 9.400 | 9.400 | 0.000 | 9.400 | 3 |
| 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: | 25.125 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.179 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 54.93 | 45.07 |
| According to VolSite | |
| HET Code: | 0R3 |
|---|---|
| Formula: | C25H28Cl2NO4 |
| Molecular weight: | 477.400 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.4 % |
| Polar Surface area: | 80.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -14.5675 | 0.435219 | -16.6641 |
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 |
| C11 | CD2 | LEU- 54 | 4.05 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 54 | 4.02 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 54 | 3.45 | 0 | Hydrophobic |
| CL1 | CB | LEU- 57 | 3.97 | 0 | Hydrophobic |
| C11 | CB | LEU- 57 | 4.42 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 61 | 3.78 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 61 | 3.66 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 61 | 3.91 | 0 | Hydrophobic |
| C21 | CG | MET- 62 | 4 | 0 | Hydrophobic |
| C22 | SD | MET- 62 | 4.16 | 0 | Hydrophobic |
| C19 | CD1 | TYR- 67 | 3.68 | 0 | Hydrophobic |
| CL1 | CE2 | PHE- 86 | 4.33 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 91 | 4.4 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 93 | 3.43 | 0 | Hydrophobic |
| C8 | CB | VAL- 93 | 4.06 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 93 | 4.28 | 0 | Hydrophobic |
| O2 | NZ | LYS- 94 | 3.18 | 121.64 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 94 | 3.18 | 0 | Ionic (Protein Cationic) |
| DuAr | DuAr | HIS- 96 | 3.88 | 0 | Aromatic Face/Face |
| CL2 | CB | HIS- 96 | 3.49 | 0 | Hydrophobic |
| C21 | CD | ARG- 97 | 4.18 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 99 | 4.42 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 99 | 3.61 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 99 | 4 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 99 | 4.02 | 0 | Hydrophobic |
| CL2 | CE1 | TYR- 100 | 3.57 | 0 | Hydrophobic |
