sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.490 Å
X-ray
2012-08-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.810 | 7.810 | 7.810 | 0.000 | 7.810 | 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: | 14.028 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.574 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.55 | 58.45 |
| According to VolSite | |
| HET Code: | R45 |
|---|---|
| Formula: | C29H29BrN4O10P |
| Molecular weight: | 704.439 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.08 % |
| Polar Surface area: | 257.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 17 |
| X | Y | Z |
|---|---|---|
| 7.95989 | 26.9937 | 4.22282 |
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 | 2.95 | 159.97 | H-Bond (Ligand Donor) |
| C18 | CG1 | ILE- 180 | 4.24 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 180 | 3.47 | 0 | Hydrophobic |
| O4 | N | LEU- 181 | 2.9 | 159.66 | H-Bond (Protein Donor) |
| C32 | CD2 | LEU- 181 | 4.4 | 0 | Hydrophobic |
| C24 | CB | HIS- 183 | 3.51 | 0 | Hydrophobic |
| C8 | CB | LEU- 214 | 4.4 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 218 | 3.69 | 0 | Aromatic Face/Face |
| C12 | CB | HIS- 218 | 3.95 | 0 | Hydrophobic |
| O2 | OE1 | GLU- 219 | 2.61 | 163.73 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 235 | 4.18 | 0 | Hydrophobic |
| C10 | CB | PHE- 237 | 4.38 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 3.38 | 148.03 | H-Bond (Ligand Donor) |
| C27 | CG2 | THR- 239 | 4.38 | 0 | Hydrophobic |
| O7 | N | TYR- 240 | 2.69 | 161.23 | H-Bond (Protein Donor) |
| N4 | O | TYR- 240 | 2.97 | 137.09 | H-Bond (Ligand Donor) |
| C12 | CB | TYR- 240 | 3.94 | 0 | Hydrophobic |
| O3 | ZN | ZN- 301 | 1.91 | 0 | Metal Acceptor |
