sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-10-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.160 | 7.100 | 7.140 | 0.580 | 8.190 | 10 |
| 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: | 17.910 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.232 | 290.250 |
| % Hydrophobic | % Polar |
|---|---|
| 68.60 | 31.40 |
| According to VolSite | |
| HET Code: | NUT |
|---|---|
| Formula: | C30H31Cl2N4O4 |
| Molecular weight: | 582.498 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.66 % |
| Polar Surface area: | 85.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -23.8346 | 7.5297 | -14.0528 |
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 |
| CL1 | CD1 | LEU- 54 | 4.13 | 0 | Hydrophobic |
| CL | CD1 | LEU- 54 | 3.69 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 54 | 3.81 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 54 | 3.89 | 0 | Hydrophobic |
| CL1 | CB | LEU- 57 | 4.23 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 61 | 3.76 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 61 | 3.55 | 0 | Hydrophobic |
| C8 | SD | MET- 62 | 4.42 | 0 | Hydrophobic |
| C8 | CB | TYR- 67 | 4.17 | 0 | Hydrophobic |
| C7 | CB | TYR- 67 | 4.29 | 0 | Hydrophobic |
| C | CB | GLN- 72 | 4.25 | 0 | Hydrophobic |
| C4 | CB | GLN- 72 | 4.29 | 0 | Hydrophobic |
| C1 | CB | HIS- 73 | 4.48 | 0 | Hydrophobic |
| C | CB | HIS- 73 | 3.99 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 75 | 3.72 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 91 | 4.04 | 0 | Hydrophobic |
| C13 | CB | VAL- 93 | 4.42 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 93 | 4.12 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 93 | 3.79 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 93 | 3.55 | 0 | Hydrophobic |
| CL | CB | HIS- 96 | 3.71 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 96 | 3.93 | 0 | Aromatic Face/Face |
| CL1 | CG2 | ILE- 99 | 4.26 | 0 | Hydrophobic |
| CL | CG2 | ILE- 99 | 4.28 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 99 | 3.86 | 0 | Hydrophobic |
| CL | CE1 | TYR- 100 | 3.71 | 0 | Hydrophobic |
