sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.150 Å
X-ray
2012-08-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.590 | 9.640 | 9.620 | 0.060 | 9.720 | 3 |
| 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: | 12.577 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.823 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.21 | 54.79 |
| According to VolSite | |
| HET Code: | R47 |
|---|---|
| Formula: | C35H32BrClN4O10P |
| Molecular weight: | 814.980 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.41 % |
| Polar Surface area: | 257.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 6.99796 | 26.6842 | 4.17702 |
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 | 2.96 | 155.61 | H-Bond (Ligand Donor) |
| C18 | CG1 | ILE- 180 | 4.26 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 180 | 3.92 | 0 | Hydrophobic |
| O4 | N | LEU- 181 | 2.83 | 164.82 | H-Bond (Protein Donor) |
| C33 | CD2 | LEU- 181 | 3.5 | 0 | Hydrophobic |
| C20 | CB | HIS- 183 | 3.56 | 0 | Hydrophobic |
| C10 | CB | LEU- 214 | 4.27 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 218 | 3.92 | 0 | Aromatic Face/Face |
| C12 | CB | HIS- 218 | 3.83 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 219 | 2.56 | 174.31 | H-Bond (Protein Donor) |
| C7 | CG2 | VAL- 235 | 4.41 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 235 | 3.93 | 0 | Hydrophobic |
| CL1 | CB | PHE- 237 | 4.13 | 0 | Hydrophobic |
| C2 | CB | PHE- 237 | 4.41 | 0 | Hydrophobic |
| O7 | N | TYR- 240 | 2.93 | 163.72 | H-Bond (Protein Donor) |
| N4 | O | TYR- 240 | 3.31 | 129.66 | H-Bond (Ligand Donor) |
| C12 | CB | TYR- 240 | 3.93 | 0 | Hydrophobic |
| CL1 | CD | LYS- 241 | 4.49 | 0 | Hydrophobic |
| C2 | CB | LYS- 241 | 4.11 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 243 | 3.98 | 0 | Hydrophobic |
| O2 | ZN | ZN- 301 | 1.83 | 0 | Metal Acceptor |
