sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2004-04-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.100 | 7.140 | 7.140 | 0.040 | 7.170 | 2 |
| 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: | 26.445 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.277 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.12 | 41.88 |
| According to VolSite | |
| HET Code: | DIZ |
|---|---|
| Formula: | C23H14Cl2IN2O4 |
| Molecular weight: | 580.179 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.91 % |
| Polar Surface area: | 89.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 43.6278 | 12.2999 | 28.9978 |
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 |
| C2 | CA | GLY- 16 | 3.77 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 54 | 3.65 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 54 | 3.99 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 54 | 4.09 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 57 | 4.32 | 0 | Hydrophobic |
| C22 | CB | LEU- 57 | 3.96 | 0 | Hydrophobic |
| I1 | CG2 | ILE- 61 | 4.48 | 0 | Hydrophobic |
| CL2 | CD1 | ILE- 61 | 3.55 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 61 | 3.76 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 61 | 3.62 | 0 | Hydrophobic |
| C13 | CE | MET- 62 | 3.54 | 0 | Hydrophobic |
| I1 | CB | TYR- 67 | 3.89 | 0 | Hydrophobic |
| CL2 | CE2 | PHE- 86 | 4.25 | 0 | Hydrophobic |
| CL2 | CZ | PHE- 91 | 3.93 | 0 | Hydrophobic |
| C5 | CB | VAL- 93 | 4.46 | 0 | Hydrophobic |
| I1 | CG1 | VAL- 93 | 3.99 | 0 | Hydrophobic |
| C19 | CB | VAL- 93 | 4.44 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 93 | 4.3 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 93 | 3.94 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 96 | 3.94 | 0 | Aromatic Face/Face |
| CL1 | CB | HIS- 96 | 3.51 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 99 | 4.13 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 99 | 4.33 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 99 | 3.99 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 99 | 3.66 | 0 | Hydrophobic |
| CL1 | CD1 | TYR- 100 | 3.65 | 0 | Hydrophobic |
| O4 | O | HOH- 120 | 3.29 | 179.98 | H-Bond (Protein Donor) |
