sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2009-07-08
| 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: | 28.849 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.954 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.24 | 50.76 |
| According to VolSite | |
| HET Code: | 518 |
|---|---|
| Formula: | C29H29N3O5 |
| Molecular weight: | 499.558 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.4 % |
| Polar Surface area: | 113.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -7.95311 | 28.5626 | 51.4913 |
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 |
| O13 | N | LEU- 185 | 2.95 | 175.51 | H-Bond (Protein Donor) |
| C2 | CB | HIS- 222 | 3.3 | 0 | Hydrophobic |
| C4 | CB | HIS- 222 | 3.94 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 222 | 3.97 | 0 | Aromatic Face/Face |
| C2 | CD1 | LEU- 239 | 4.14 | 0 | Hydrophobic |
| N20 | O | LEU- 239 | 3.42 | 126.05 | H-Bond (Ligand Donor) |
| C23 | CG1 | ILE- 243 | 3.32 | 0 | Hydrophobic |
| C5 | CB | TYR- 244 | 4.42 | 0 | Hydrophobic |
| O29 | N | THR- 245 | 2.75 | 144.01 | H-Bond (Protein Donor) |
| C32 | CG2 | THR- 247 | 3.31 | 0 | Hydrophobic |
| C36 | CG2 | THR- 247 | 3.93 | 0 | Hydrophobic |
| C37 | CB | THR- 247 | 3.73 | 0 | Hydrophobic |
| C37 | CD1 | PHE- 252 | 3.43 | 0 | Hydrophobic |
| C34 | CG | PRO- 255 | 3.24 | 0 | Hydrophobic |
