sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-10-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.120 | 7.120 | 7.120 | 0.000 | 7.120 | 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: | 9.996 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.112 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 43.75 | 56.25 |
| According to VolSite | |
| HET Code: | 3EJ |
|---|---|
| Formula: | C22H16FN6O3 |
| Molecular weight: | 431.399 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.25 % |
| Polar Surface area: | 125.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 45.9542 | 22.7251 | 17.9093 |
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 |
| O9 | NZ | LYS- 140 | 2.77 | 155.06 | H-Bond (Protein Donor) |
| O9 | NZ | LYS- 140 | 2.77 | 0 | Ionic (Protein Cationic) |
| O8 | ND2 | ASN- 215 | 3 | 148.96 | H-Bond (Protein Donor) |
| C27 | CG | LEU- 218 | 4.13 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 218 | 3.64 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 219 | 4.05 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 222 | 4 | 0 | Aromatic Face/Face |
| C29 | CB | HIS- 222 | 3.61 | 0 | Hydrophobic |
| N23 | O | ALA- 238 | 3.23 | 128.35 | H-Bond (Ligand Donor) |
| C27 | CD1 | LEU- 239 | 4.38 | 0 | Hydrophobic |
| C30 | CB | TYR- 244 | 4.12 | 0 | Hydrophobic |
| O26 | N | THR- 245 | 2.9 | 166.31 | H-Bond (Protein Donor) |
| C10 | CZ | TYR- 246 | 4.49 | 0 | Hydrophobic |
| N12 | OG1 | THR- 247 | 3.14 | 148.18 | H-Bond (Protein Donor) |
| N12 | N | THR- 247 | 3.16 | 134.49 | H-Bond (Protein Donor) |
| N13 | OG1 | THR- 247 | 3.23 | 171.75 | H-Bond (Protein Donor) |
| N13 | N | THR- 247 | 2.84 | 166.06 | H-Bond (Protein Donor) |
| N15 | OG1 | THR- 247 | 3.46 | 134.46 | H-Bond (Protein Donor) |
| C16 | CG2 | THR- 247 | 4.1 | 0 | Hydrophobic |
| C10 | CB | LYS- 249 | 4.24 | 0 | Hydrophobic |
| C4 | CB | PHE- 252 | 4.2 | 0 | Hydrophobic |
