sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2012-08-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.830 | 7.830 | 7.830 | 0.000 | 7.830 | 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: | 18.425 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.988 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.24 | 51.76 |
| According to VolSite | |
| HET Code: | R4C |
|---|---|
| Formula: | C25H27BrN4O6P |
| Molecular weight: | 590.383 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.34 % |
| Polar Surface area: | 177.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -5.8117 | 25.8714 | -4.60935 |
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 | 3.09 | 147.42 | H-Bond (Ligand Donor) |
| C18 | CD1 | ILE- 180 | 4.22 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 180 | 4.01 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 180 | 4.23 | 0 | Hydrophobic |
| O4 | N | LEU- 181 | 2.86 | 168.79 | H-Bond (Protein Donor) |
| C32 | CD2 | LEU- 181 | 3.74 | 0 | Hydrophobic |
| C20 | CB | HIS- 183 | 3.58 | 0 | Hydrophobic |
| C8 | CB | LEU- 214 | 4.46 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 218 | 3.67 | 0 | Aromatic Face/Face |
| C12 | CB | HIS- 218 | 3.92 | 0 | Hydrophobic |
| O2 | OE2 | GLU- 219 | 2.61 | 166.73 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 235 | 4.05 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 3.4 | 172.27 | H-Bond (Ligand Donor) |
| O7 | N | TYR- 240 | 2.83 | 150.16 | H-Bond (Protein Donor) |
| C12 | CB | TYR- 240 | 4.14 | 0 | Hydrophobic |
| O3 | ZN | ZN- 301 | 1.92 | 0 | Metal Acceptor |
