sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2001-01-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.300 | 8.300 | 8.300 | 0.000 | 8.300 | 1 |
| Name: | Stromelysin-3 |
|---|---|
| ID: | MMP11_MOUSE |
| AC: | Q02853 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 3.4.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 12 % |
| F | 88 % |
| B-Factor: | 26.977 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.514 | 543.375 |
| % Hydrophobic | % Polar |
|---|---|
| 36.65 | 63.35 |
| According to VolSite | |
| HET Code: | RXP |
|---|---|
| Formula: | C39H42N4O6P |
| Molecular weight: | 693.748 g/mol |
| DrugBank ID: | DB04318 |
| Buried Surface Area: | 45.53 % |
| Polar Surface area: | 176.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 111.546 | 116.432 | 74.9098 |
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 |
| C28 | CD2 | LEU- 172 | 3.86 | 0 | Hydrophobic |
| C31 | CG | LEU- 172 | 4.35 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 172 | 3.52 | 0 | Hydrophobic |
| N1 | O | GLY- 179 | 2.64 | 161.96 | H-Bond (Ligand Donor) |
| C21 | CG2 | ILE- 180 | 4.39 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 180 | 3.47 | 0 | Hydrophobic |
| O2 | N | LEU- 181 | 2.7 | 159.98 | H-Bond (Protein Donor) |
| C38 | CD1 | LEU- 181 | 4.28 | 0 | Hydrophobic |
| C28 | CB | HIS- 183 | 4.35 | 0 | Hydrophobic |
| C26 | CB | HIS- 183 | 3.86 | 0 | Hydrophobic |
| C28 | CB | PHE- 185 | 4.35 | 0 | Hydrophobic |
| C18 | CB | GLN- 215 | 3.92 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 216 | 4.1 | 0 | Hydrophobic |
| C38 | CG2 | VAL- 216 | 4.34 | 0 | Hydrophobic |
| C14 | CB | HIS- 219 | 3.92 | 0 | Hydrophobic |
| O2P | OE1 | GLU- 220 | 2.6 | 162.03 | H-Bond (Protein Donor) |
| C17 | CD1 | LEU- 236 | 4.1 | 0 | Hydrophobic |
| C16 | CB | SER- 238 | 4.37 | 0 | Hydrophobic |
| N2 | O | PRO- 239 | 3.22 | 164.51 | H-Bond (Ligand Donor) |
| C2 | CD2 | PHE- 240 | 4.27 | 0 | Hydrophobic |
| O1 | N | TYR- 241 | 2.93 | 166.98 | H-Bond (Protein Donor) |
| C38 | CB | TYR- 241 | 4.33 | 0 | Hydrophobic |
| C14 | CB | TYR- 241 | 4.04 | 0 | Hydrophobic |
| C19 | CB | TYR- 241 | 3.86 | 0 | Hydrophobic |
| O1P | ZN | ZN- 5517 | 2.31 | 0 | Metal Acceptor |
