sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2012-08-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.550 | 9.550 | 9.550 | 0.000 | 9.550 | 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: | 17.777 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.604 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 47.11 | 52.89 |
| According to VolSite | |
| HET Code: | R4B |
|---|---|
| Formula: | C31H30BrClN4O6P |
| Molecular weight: | 700.924 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.7 % |
| Polar Surface area: | 177.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -5.95434 | 25.4273 | -4.44998 |
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 | 2.9 | 163.74 | H-Bond (Ligand Donor) |
| C18 | CD1 | ILE- 180 | 3.86 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 180 | 4.28 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 180 | 3.95 | 0 | Hydrophobic |
| O4 | N | LEU- 181 | 2.8 | 171.31 | H-Bond (Protein Donor) |
| C32 | CD2 | LEU- 181 | 4.23 | 0 | Hydrophobic |
| C24 | CB | HIS- 183 | 3.55 | 0 | Hydrophobic |
| C10 | CB | LEU- 214 | 4.39 | 0 | Hydrophobic |
| C12 | CB | HIS- 218 | 3.85 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 219 | 2.66 | 165.12 | H-Bond (Protein Donor) |
| C10 | CG2 | VAL- 235 | 4.15 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 235 | 3.82 | 0 | Hydrophobic |
| C8 | CB | PHE- 237 | 4.5 | 0 | Hydrophobic |
| C5 | CB | PHE- 237 | 4.39 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 3.39 | 155.55 | H-Bond (Ligand Donor) |
| C27 | CG2 | THR- 239 | 4.28 | 0 | Hydrophobic |
| O7 | N | TYR- 240 | 2.78 | 150.06 | H-Bond (Protein Donor) |
| N4 | O | TYR- 240 | 3.22 | 128.93 | H-Bond (Ligand Donor) |
| C12 | CB | TYR- 240 | 4 | 0 | Hydrophobic |
| C3 | CD | LYS- 241 | 4.08 | 0 | Hydrophobic |
| C5 | CG | LYS- 241 | 3.45 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 243 | 3.66 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 243 | 3.89 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 248 | 3.42 | 0 | Hydrophobic |
| O2 | ZN | ZN- 301 | 1.92 | 0 | Metal Acceptor |
