sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2007-02-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.190 | 7.190 | 7.190 | 0.000 | 7.190 | 1 |
| Name: | Collagenase 3 |
|---|---|
| ID: | MMP13_HUMAN |
| AC: | P45452 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.846 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.921 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.41 | 53.59 |
| According to VolSite | |
| HET Code: | SP6 |
|---|---|
| Formula: | C21H16N2O4S |
| Molecular weight: | 392.428 g/mol |
| DrugBank ID: | DB08561 |
| Buried Surface Area: | 72.78 % |
| Polar Surface area: | 92.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 52.703 | 9.86407 | 10.668 |
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 |
| S1 | CD1 | LEU- 197 | 4.14 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 197 | 4.1 | 0 | Hydrophobic |
| C12 | CG | LEU- 197 | 4.17 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 198 | 4.13 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 201 | 3.99 | 0 | Aromatic Face/Face |
| C12 | CB | HIS- 201 | 3.48 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 218 | 4 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 218 | 3.96 | 0 | Hydrophobic |
| C11 | CB | PHE- 220 | 4.28 | 0 | Hydrophobic |
| C18 | CB | TYR- 223 | 4.13 | 0 | Hydrophobic |
| O3 | N | THR- 224 | 2.84 | 160.71 | H-Bond (Protein Donor) |
| C4 | CB | THR- 226 | 4.46 | 0 | Hydrophobic |
| O2 | N | THR- 226 | 3.04 | 157.57 | H-Bond (Protein Donor) |
| C4 | CB | LYS- 228 | 4.08 | 0 | Hydrophobic |
| C13 | CB | PHE- 231 | 3.97 | 0 | Hydrophobic |
| O1 | N | MET- 232 | 2.95 | 171.34 | H-Bond (Protein Donor) |
