sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.090 Å
X-ray
2001-07-11
| 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: | 11.852 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.531 | 351.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.08 | 51.92 |
| According to VolSite | |
| HET Code: | BAT |
|---|---|
| Formula: | C23H31N3O4S2 |
| Molecular weight: | 477.640 g/mol |
| DrugBank ID: | DB03880 |
| Buried Surface Area: | 51.04 % |
| Polar Surface area: | 161.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 12.6864 | -6.30145 | 20.9805 |
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 |
| N3 | O | GLY- 179 | 2.7 | 165.06 | H-Bond (Ligand Donor) |
| C22 | CG1 | ILE- 180 | 4.09 | 0 | Hydrophobic |
| S1 | CG2 | ILE- 180 | 3.88 | 0 | Hydrophobic |
| O3 | N | LEU- 181 | 2.81 | 151.84 | H-Bond (Protein Donor) |
| C12 | CD1 | LEU- 181 | 4.26 | 0 | Hydrophobic |
| N1 | O | ALA- 182 | 2.88 | 175.28 | H-Bond (Ligand Donor) |
| C12 | CG2 | THR- 215 | 3.96 | 0 | Hydrophobic |
| C12 | CB | HIS- 218 | 4.35 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 2.88 | 154.5 | H-Bond (Ligand Donor) |
| O4 | N | TYR- 240 | 2.9 | 161.86 | H-Bond (Protein Donor) |
| C10 | CB | TYR- 240 | 4.04 | 0 | Hydrophobic |
| O1 | ZN | ZN- 400 | 2.08 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 400 | 2.08 | 0 | Metal Acceptor |
