sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2010-07-09
| Name: | Catechol O-methyltransferase |
|---|---|
| ID: | COMT_RAT |
| AC: | P22734 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.1.1.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.565 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | CL MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.332 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.12 | 43.88 |
| According to VolSite | |
| HET Code: | 637 |
|---|---|
| Formula: | C26H24FN5O6 |
| Molecular weight: | 521.497 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.82 % |
| Polar Surface area: | 162.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -2.52884 | 16.6836 | 14.1358 |
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 | CE | MET- 40 | 4.13 | 0 | Hydrophobic |
| C20 | SD | MET- 40 | 3.7 | 0 | Hydrophobic |
| C23 | CB | MET- 40 | 4.01 | 0 | Hydrophobic |
| C33 | CB | MET- 40 | 3.86 | 0 | Hydrophobic |
| O5 | OE2 | GLU- 90 | 3.08 | 128.72 | H-Bond (Ligand Donor) |
| C7 | SD | MET- 91 | 4.15 | 0 | Hydrophobic |
| N40 | N | MET- 91 | 3.11 | 142.03 | H-Bond (Protein Donor) |
| C4 | CD2 | TYR- 95 | 3.98 | 0 | Hydrophobic |
| C7 | CB | SER- 119 | 4.29 | 0 | Hydrophobic |
| N38 | N | SER- 119 | 2.98 | 150.55 | H-Bond (Protein Donor) |
| C1 | CB | HIS- 142 | 4.42 | 0 | Hydrophobic |
| C7 | CE3 | TRP- 143 | 4.47 | 0 | Hydrophobic |
| O32 | NZ | LYS- 144 | 2.95 | 167.9 | H-Bond (Protein Donor) |
| C7 | CG | ARG- 146 | 4.31 | 0 | Hydrophobic |
| O34 | ND2 | ASN- 170 | 2.72 | 137.85 | H-Bond (Protein Donor) |
| C28 | CG2 | VAL- 173 | 3.78 | 0 | Hydrophobic |
| C21 | CG | PRO- 174 | 3.74 | 0 | Hydrophobic |
| C27 | CG | PRO- 174 | 3.86 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 198 | 3.95 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 198 | 3.66 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 198 | 3.79 | 0 | Hydrophobic |
| O34 | OE1 | GLU- 199 | 3.31 | 161.39 | H-Bond (Ligand Donor) |
| O32 | MG | MG- 222 | 2.09 | 0 | Metal Acceptor |
| O34 | MG | MG- 222 | 2.15 | 0 | Metal Acceptor |
| DuAr | MG | MG- 222 | 3.99 | 96.76 | Pi/Cation |
