sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-01-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.840 | 7.780 | 7.780 | 0.940 | 8.720 | 2 |
| Name: | Macrophage metalloelastase |
|---|---|
| ID: | MMP12_HUMAN |
| AC: | P39900 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.65 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.601 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.741 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.16 | 54.84 |
| According to VolSite | |
| HET Code: | EEG |
|---|---|
| Formula: | C29H29N3O7S |
| Molecular weight: | 563.621 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.59 % |
| Polar Surface area: | 209.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 5.51873 | 26.6835 | 6.53725 |
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 |
| N1 | O | GLY- 179 | 2.95 | 144.97 | H-Bond (Ligand Donor) |
| O8 | N | GLY- 179 | 2.73 | 169.69 | H-Bond (Protein Donor) |
| O2 | N | LEU- 181 | 2.7 | 163.09 | H-Bond (Protein Donor) |
| C28 | CD1 | LEU- 181 | 4.28 | 0 | Hydrophobic |
| S7 | CB | LEU- 214 | 3.79 | 0 | Hydrophobic |
| C15 | CB | THR- 215 | 4.31 | 0 | Hydrophobic |
| C28 | CG2 | THR- 215 | 3.83 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 218 | 3.95 | 0 | Aromatic Face/Face |
| C14 | CB | HIS- 218 | 4.03 | 0 | Hydrophobic |
| C28 | CB | HIS- 218 | 4.09 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 235 | 4.37 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 3.03 | 153.23 | H-Bond (Ligand Donor) |
| O1 | N | TYR- 240 | 2.84 | 166.32 | H-Bond (Protein Donor) |
| C15 | CD1 | TYR- 240 | 3.41 | 0 | Hydrophobic |
| C15 | CB | TYR- 240 | 3.96 | 0 | Hydrophobic |
| C21 | CG | LYS- 241 | 4.09 | 0 | Hydrophobic |
| C26 | CD | LYS- 241 | 4.19 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 243 | 3.7 | 0 | Hydrophobic |
