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
2012-08-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.000 | 8.000 | 8.000 | 0.000 | 8.000 | 1 |
| 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: | 12.598 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.686 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.75 | 57.25 |
| According to VolSite | |
| HET Code: | KLJ |
|---|---|
| Formula: | C11H16N2O5S |
| Molecular weight: | 288.320 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.91 % |
| Polar Surface area: | 113.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 3.49884 | -5.20684 | 6.21021 |
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 | CD1 | ILE- 180 | 3.81 | 0 | Hydrophobic |
| C1 | CB | LEU- 181 | 4.41 | 0 | Hydrophobic |
| O3 | N | LEU- 181 | 2.99 | 123.92 | H-Bond (Protein Donor) |
| N2 | O | ALA- 182 | 2.58 | 122.52 | H-Bond (Ligand Donor) |
| O3 | N | ALA- 182 | 3.22 | 167.04 | H-Bond (Protein Donor) |
| C3 | CG2 | THR- 215 | 4.11 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 218 | 3.84 | 0 | Aromatic Face/Face |
| C4 | CB | HIS- 218 | 3.84 | 0 | Hydrophobic |
| O4 | OE1 | GLU- 219 | 2.57 | 164.07 | H-Bond (Protein Donor) |
| C9 | CG2 | VAL- 235 | 4.09 | 0 | Hydrophobic |
| C4 | CB | TYR- 240 | 3.91 | 0 | Hydrophobic |
| O2 | ZN | ZN- 301 | 2.15 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 301 | 2.37 | 0 | Metal Acceptor |
