sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.870 Å
X-ray
2005-06-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.220 | 9.220 | 9.220 | 0.000 | 9.220 | 1 |
| Name: | Neutrophil collagenase |
|---|---|
| ID: | MMP8_HUMAN |
| AC: | P22894 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.34 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.976 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.307 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.00 | 60.00 |
| According to VolSite | |
| HET Code: | FIN |
|---|---|
| Formula: | C17H20NO6PS |
| Molecular weight: | 397.383 g/mol |
| DrugBank ID: | DB07772 |
| Buried Surface Area: | 63.65 % |
| Polar Surface area: | 136.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -1.93212 | 24.4382 | 8.14554 |
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 |
| C12 | CD1 | ILE- 159 | 3.35 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 159 | 4.12 | 0 | Hydrophobic |
| C6 | CB | LEU- 160 | 4.29 | 0 | Hydrophobic |
| O3 | N | LEU- 160 | 2.6 | 138.74 | H-Bond (Protein Donor) |
| O3 | N | ALA- 161 | 3.05 | 158.47 | H-Bond (Protein Donor) |
| C13 | CB | HIS- 162 | 3.61 | 0 | Hydrophobic |
| C16 | CB | LEU- 193 | 4.23 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 193 | 4.05 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 194 | 4.47 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 194 | 3.91 | 0 | Hydrophobic |
| C14 | CB | HIS- 197 | 3.86 | 0 | Hydrophobic |
| C15 | CB | HIS- 197 | 3.59 | 0 | Hydrophobic |
| O5 | OE2 | GLU- 198 | 2.87 | 159.84 | H-Bond (Protein Donor) |
| C3 | CD1 | LEU- 214 | 3.52 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 214 | 3.7 | 0 | Hydrophobic |
| C14 | CB | TYR- 219 | 3.78 | 0 | Hydrophobic |
| C3 | CG | ARG- 222 | 3.94 | 0 | Hydrophobic |
| O6 | ZN | ZN- 999 | 1.98 | 0 | Metal Acceptor |
