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
2003-07-29
| Name: | Stromelysin-2 |
|---|---|
| ID: | MMP10_HUMAN |
| AC: | P09238 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 19 % |
| C | 81 % |
| B-Factor: | 37.078 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 1620.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.54 | 51.46 |
| According to VolSite | |
| HET Code: | NGH |
|---|---|
| Formula: | C13H20N2O5S |
| Molecular weight: | 316.373 g/mol |
| DrugBank ID: | DB08271 |
| Buried Surface Area: | 71.07 % |
| Polar Surface area: | 104.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 23.0719 | -24.2489 | 8.74767 |
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 |
| C13 | CB | SER- 179 | 3.42 | 0 | Hydrophobic |
| C14 | CB | SER- 179 | 3.45 | 0 | Hydrophobic |
| C12 | CB | SER- 179 | 3.39 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 180 | 4.01 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 180 | 3.8 | 0 | Hydrophobic |
| O2 | N | LEU- 180 | 2.73 | 139.44 | H-Bond (Protein Donor) |
| N1 | O | ALA- 181 | 2.93 | 146.83 | H-Bond (Ligand Donor) |
| C13 | CB | HIS- 182 | 4.25 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 214 | 4.01 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 214 | 3.85 | 0 | Hydrophobic |
| C7 | CB | HIS- 217 | 3.8 | 0 | Hydrophobic |
| C3 | CB | HIS- 217 | 4.18 | 0 | Hydrophobic |
| C1 | CB | PRO- 237 | 4.06 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 238 | 3.81 | 0 | Hydrophobic |
| C1 | CD2 | TYR- 239 | 3.55 | 0 | Hydrophobic |
| C2 | CB | TYR- 239 | 3.36 | 0 | Hydrophobic |
| C13 | CB | PHE- 242 | 3.44 | 0 | Hydrophobic |
| O4 | ZN | ZN- 474 | 2.36 | 0 | Metal Acceptor |
| O5 | ZN | ZN- 474 | 2.79 | 0 | Metal Acceptor |
