sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2010-07-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.890 | 9.890 | 9.890 | 0.000 | 9.890 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 13.381 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.913 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 37.02 | 62.98 |
| According to VolSite | |
| HET Code: | 3O2 |
|---|---|
| Formula: | C26H32F3N6O7S |
| Molecular weight: | 629.628 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.03 % |
| Polar Surface area: | 167.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 7.48688 | 83.3168 | 77.6753 |
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 |
| C4 | CD2 | LEU- 2184 | 3.72 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 2184 | 4.09 | 0 | Hydrophobic |
| O2 | N | LEU- 2185 | 2.95 | 146.82 | H-Bond (Protein Donor) |
| C10 | CD1 | LEU- 2185 | 4.14 | 0 | Hydrophobic |
| N2 | O | ALA- 2186 | 2.74 | 136.64 | H-Bond (Ligand Donor) |
| O2 | N | ALA- 2186 | 2.98 | 146.47 | H-Bond (Protein Donor) |
| C23 | CD2 | LEU- 2218 | 3.84 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 2219 | 4.06 | 0 | Hydrophobic |
| C15 | CB | HIS- 2222 | 4.03 | 0 | Hydrophobic |
| C17 | CB | HIS- 2222 | 4.2 | 0 | Hydrophobic |
| O6 | OE2 | GLU- 2223 | 2.56 | 162.2 | H-Bond (Protein Donor) |
| C17 | CD1 | LEU- 2239 | 4.1 | 0 | Hydrophobic |
| C5 | CB | PRO- 2242 | 4.09 | 0 | Hydrophobic |
| C14 | CB | TYR- 2244 | 4.02 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 2252 | 3.46 | 0 | Hydrophobic |
| F1 | CB | MET- 2253 | 3.74 | 0 | Hydrophobic |
| O7 | N | MET- 2253 | 3.32 | 170.14 | H-Bond (Protein Donor) |
| C25 | CG | PRO- 2255 | 4.05 | 0 | Hydrophobic |
| O5 | ZN | ZN- 2999 | 2.07 | 0 | Metal Acceptor |
| O6 | ZN | ZN- 2999 | 2.19 | 0 | Metal Acceptor |
