sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 Å
X-ray
1995-08-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.640 | 6.640 | 6.640 | 0.000 | 6.640 | 3 |
| 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: | 10.193 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.153 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.53 | 56.47 |
| According to VolSite | |
| HET Code: | INH |
|---|---|
| Formula: | C25H35N6O4 |
| Molecular weight: | 483.583 g/mol |
| DrugBank ID: | DB02747 |
| Buried Surface Area: | 47.82 % |
| Polar Surface area: | 178.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| -16.9532 | 94.6668 | 80.9449 |
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 |
| N29 | O | ASN- 162 | 2.92 | 155.06 | H-Bond (Ligand Donor) |
| C21 | CG2 | VAL- 163 | 4.28 | 0 | Hydrophobic |
| O17 | N | LEU- 164 | 2.79 | 167.46 | H-Bond (Protein Donor) |
| C35 | CD1 | LEU- 164 | 4.24 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 164 | 3.61 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 198 | 3.88 | 0 | Hydrophobic |
| C13 | CB | HIS- 201 | 3.6 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 202 | 2.81 | 164.43 | H-Bond (Ligand Donor) |
| N6 | OE2 | GLU- 202 | 2.81 | 0 | Ionic (Ligand Cationic) |
| C13 | CD1 | LEU- 218 | 4.06 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 222 | 3.93 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 222 | 4.19 | 0 | Hydrophobic |
| O28 | N | TYR- 223 | 2.91 | 170.24 | H-Bond (Protein Donor) |
| C34 | CD2 | TYR- 223 | 3.36 | 0 | Hydrophobic |
| C35 | CB | TYR- 223 | 3.63 | 0 | Hydrophobic |
| C15 | CB | TYR- 223 | 3.62 | 0 | Hydrophobic |
| O4 | O | HOH- 301 | 3.12 | 145.98 | H-Bond (Protein Donor) |
