sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.640 Å
X-ray
1999-04-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 7.720 | 7.720 | 0.000 | 7.720 | 1 |
| Name: | Stromelysin-1 |
|---|---|
| ID: | MMP3_HUMAN |
| AC: | P08254 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 11.177 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.546 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 38.76 | 61.24 |
| According to VolSite | |
| HET Code: | DPS |
|---|---|
| Formula: | C28H28N3O4S |
| Molecular weight: | 502.605 g/mol |
| DrugBank ID: | DB02449 |
| Buried Surface Area: | 64.17 % |
| Polar Surface area: | 113.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 27.2837 | 48.6593 | -1.11939 |
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 |
| C20 | CG1 | VAL- 163 | 3.87 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 164 | 4.18 | 0 | Hydrophobic |
| O1 | N | LEU- 164 | 2.79 | 157.9 | H-Bond (Protein Donor) |
| O1 | N | ALA- 165 | 3.39 | 145.39 | H-Bond (Protein Donor) |
| C20 | CB | HIS- 166 | 3.81 | 0 | Hydrophobic |
| C13 | CB | LEU- 197 | 3.85 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 197 | 3.75 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 198 | 4.37 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 198 | 4.28 | 0 | Hydrophobic |
| C6 | CB | HIS- 201 | 4.45 | 0 | Hydrophobic |
| C15 | CB | HIS- 201 | 3.74 | 0 | Hydrophobic |
| O3 | OE2 | GLU- 202 | 2.57 | 144.45 | H-Bond (Protein Donor) |
| C21 | CE1 | PHE- 210 | 3.28 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 218 | 4.39 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 218 | 4.12 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 223 | 3.86 | 0 | Hydrophobic |
| C2 | CB | TYR- 223 | 3.85 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 224 | 4 | 0 | Aromatic Edge/Face |
| C10 | CD2 | LEU- 226 | 4.23 | 0 | Hydrophobic |
| C12 | CG | LEU- 226 | 4 | 0 | Hydrophobic |
| O3 | ZN | ZN- 301 | 2.62 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 301 | 2.09 | 0 | Metal Acceptor |
