sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
1994-01-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.700 | 8.700 | 0.000 | 8.700 | 2 |
| 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: | 7.311 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.440 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.64 | 56.36 |
| According to VolSite | |
| HET Code: | PLH |
|---|---|
| Formula: | C18H27N3O4 |
| Molecular weight: | 349.425 g/mol |
| DrugBank ID: | DB08403 |
| Buried Surface Area: | 56.56 % |
| Polar Surface area: | 107.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -4.58528 | 28.3805 | 22.0034 |
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 | 2.76 | 170.67 | H-Bond (Ligand Donor) |
| C2 | CD1 | ILE- 180 | 4.37 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 180 | 3.24 | 0 | Hydrophobic |
| O3 | N | LEU- 181 | 2.85 | 161.75 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 181 | 4.4 | 0 | Hydrophobic |
| N1 | O | ALA- 182 | 2.99 | 161.13 | H-Bond (Ligand Donor) |
| C7 | CG2 | VAL- 215 | 3.89 | 0 | Hydrophobic |
| C7 | CB | HIS- 218 | 4.09 | 0 | Hydrophobic |
| N2 | O | PRO- 238 | 2.9 | 172.29 | H-Bond (Ligand Donor) |
| C5 | CB | TYR- 240 | 4.25 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 240 | 4.4 | 0 | Hydrophobic |
| O4 | N | TYR- 240 | 2.94 | 175.93 | H-Bond (Protein Donor) |
| O1 | ZN | ZN- 281 | 2.29 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 281 | 2.11 | 0 | Metal Acceptor |
