sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2011-08-10
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 9.659 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.087 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 41.88 | 58.12 |
| According to VolSite | |
| HET Code: | E41 |
|---|---|
| Formula: | C20H28N2O4S |
| Molecular weight: | 392.512 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.86 % |
| Polar Surface area: | 95.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 18.2042 | 2.22411 | 60.5003 |
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 |
| CG1 | CD2 | LEU- 184 | 3.38 | 0 | Hydrophobic |
| O3 | N | LEU- 185 | 2.86 | 179.88 | H-Bond (Protein Donor) |
| C7 | CB | LEU- 185 | 3.91 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 185 | 3.99 | 0 | Hydrophobic |
| N1 | O | ALA- 186 | 2.86 | 161.54 | H-Bond (Ligand Donor) |
| C12 | CG1 | VAL- 219 | 3.85 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 222 | 3.91 | 0 | Aromatic Face/Face |
| DuAr | DuAr | HIS- 222 | 3.91 | 0 | Aromatic Face/Face |
| C12 | CB | HIS- 222 | 3.6 | 0 | Hydrophobic |
| O1 | OE2 | GLU- 223 | 2.51 | 156.09 | H-Bond (Protein Donor) |
| C18 | CB | PRO- 242 | 4.2 | 0 | Hydrophobic |
| C20 | CB | PRO- 242 | 3.72 | 0 | Hydrophobic |
| C14 | CB | TYR- 244 | 4.02 | 0 | Hydrophobic |
| O1 | ZN | ZN- 300 | 2.21 | 0 | Metal Acceptor |
| O | ZN | ZN- 300 | 2.03 | 0 | Metal Acceptor |
