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
1999-07-29
| 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 | 6 % |
| B | 94 % |
| B-Factor: | 15.736 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.915 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.21 | 54.79 |
| According to VolSite | |
| HET Code: | TR1 |
|---|---|
| Formula: | C24H32N3O4S |
| Molecular weight: | 458.594 g/mol |
| DrugBank ID: | DB08643 |
| Buried Surface Area: | 59.35 % |
| Polar Surface area: | 139.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -15.557 | -10.6737 | 5.33725 |
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 |
| CB | CG | PRO- 87 | 3.42 | 0 | Hydrophobic |
| N3 | O | ASN- 162 | 2.93 | 140.46 | H-Bond (Ligand Donor) |
| O | N | LEU- 164 | 3.16 | 164.88 | H-Bond (Protein Donor) |
| C47 | CD1 | LEU- 164 | 4.48 | 0 | Hydrophobic |
| CM3 | CD2 | LEU- 164 | 3.46 | 0 | Hydrophobic |
| C42 | CB | LEU- 197 | 3.99 | 0 | Hydrophobic |
| C50 | CG2 | VAL- 198 | 4.4 | 0 | Hydrophobic |
| C48 | CG1 | VAL- 198 | 3.8 | 0 | Hydrophobic |
| N | NE2 | HIS- 201 | 2.69 | 163.79 | H-Bond (Ligand Donor) |
| DuAr | DuAr | HIS- 201 | 3.8 | 0 | Aromatic Face/Face |
| C50 | CB | HIS- 201 | 3.94 | 0 | Hydrophobic |
| C46 | CD1 | LEU- 218 | 4.24 | 0 | Hydrophobic |
| N2 | O | PRO- 221 | 2.99 | 165.54 | H-Bond (Ligand Donor) |
| CG1 | CB | LEU- 222 | 3.79 | 0 | Hydrophobic |
| O2 | N | TYR- 223 | 2.67 | 170.28 | H-Bond (Protein Donor) |
| C42 | CD1 | TYR- 223 | 3.41 | 0 | Hydrophobic |
| C50 | CD1 | TYR- 223 | 3.31 | 0 | Hydrophobic |
| C51 | CB | TYR- 223 | 3.86 | 0 | Hydrophobic |
