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
2008-09-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.720 | 9.720 | 9.720 | 0.000 | 9.720 | 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 | 6 % |
| B | 94 % |
| B-Factor: | 18.503 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.066 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.21 | 48.79 |
| According to VolSite | |
| HET Code: | 24F |
|---|---|
| Formula: | C23H29N2O7S2 |
| Molecular weight: | 509.616 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.07 % |
| Polar Surface area: | 161.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 19.0361 | 3.94059 | 61.0597 |
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 |
| C32 | CE1 | TYR- 176 | 3.96 | 0 | Hydrophobic |
| C33 | CZ | TYR- 176 | 4.07 | 0 | Hydrophobic |
| C34 | CD2 | TYR- 176 | 3.8 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 184 | 3.6 | 0 | Hydrophobic |
| S13 | CD1 | LEU- 185 | 4.42 | 0 | Hydrophobic |
| O17 | N | LEU- 185 | 2.85 | 169.1 | H-Bond (Protein Donor) |
| C23 | CB | HIS- 187 | 3.94 | 0 | Hydrophobic |
| C27 | CB | HIS- 187 | 4.19 | 0 | Hydrophobic |
| C34 | CB | HIS- 187 | 3.97 | 0 | Hydrophobic |
| C33 | CD2 | PHE- 189 | 4.26 | 0 | Hydrophobic |
| C34 | CZ | PHE- 189 | 3.68 | 0 | Hydrophobic |
| C33 | CG | PRO- 193 | 4.43 | 0 | Hydrophobic |
| C02 | CG | LEU- 218 | 4.11 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 218 | 4.35 | 0 | Hydrophobic |
| C03 | CG2 | VAL- 219 | 4.01 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 222 | 3.73 | 0 | Aromatic Face/Face |
| C03 | CB | HIS- 222 | 3.59 | 0 | Hydrophobic |
| C01 | CD1 | LEU- 239 | 4.25 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 239 | 4.18 | 0 | Hydrophobic |
| C05 | CB | TYR- 244 | 4.2 | 0 | Hydrophobic |
| OM0 | ZN | ZN- 300 | 2.7 | 0 | Metal Acceptor |
| O21 | ZN | ZN- 300 | 1.91 | 0 | Metal Acceptor |
