sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-06-18
| Name: | Precorrin-2 methyltransferase |
|---|---|
| ID: | O27402_METTH |
| AC: | O27402 |
| Organism: | Methanothermobacter thermautotrophicus |
| Reign: | Archaea |
| TaxID: | 187420 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B | 0 % |
| B-Factor: | 28.857 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.262 | 1225.125 |
| % Hydrophobic | % Polar |
|---|---|
| 35.81 | 64.19 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 82.34 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -23.675 | 38.447 | -4.18331 |
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 |
| N6 | O | PRO- 12 | 2.77 | 127.55 | H-Bond (Ligand Donor) |
| N | O | ASP- 104 | 3.06 | 137.28 | H-Bond (Ligand Donor) |
| O | N | ASP- 104 | 2.98 | 175.8 | H-Bond (Protein Donor) |
| N | O | ILE- 107 | 2.68 | 164.7 | H-Bond (Ligand Donor) |
| SD | CB | TYR- 108 | 3.87 | 0 | Hydrophobic |
| CB | CB | TYR- 108 | 4.4 | 0 | Hydrophobic |
| O | OG1 | THR- 132 | 2.72 | 155.28 | H-Bond (Protein Donor) |
| OXT | N | SER- 133 | 2.85 | 156.04 | H-Bond (Protein Donor) |
| C1' | CB | SER- 133 | 4.07 | 0 | Hydrophobic |
| CB | CE | MET- 175 | 4.15 | 0 | Hydrophobic |
| SD | CE | MET- 175 | 4.39 | 0 | Hydrophobic |
| C4' | CE | MET- 175 | 4.3 | 0 | Hydrophobic |
| C1' | CE | MET- 175 | 4.28 | 0 | Hydrophobic |
| O3' | N | LYS- 176 | 3.02 | 128.61 | H-Bond (Protein Donor) |
| O2' | N | LYS- 176 | 3.03 | 129.98 | H-Bond (Protein Donor) |
| N6 | O | CYS- 203 | 3.26 | 146.32 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 203 | 2.94 | 129.45 | H-Bond (Protein Donor) |
| C5' | CZ | TYR- 220 | 3.98 | 0 | Hydrophobic |
| C3' | CE1 | TYR- 220 | 4.29 | 0 | Hydrophobic |
| O3' | O | TYR- 220 | 3.21 | 153.04 | H-Bond (Ligand Donor) |
| C3' | CD2 | LEU- 221 | 4.25 | 0 | Hydrophobic |
| O2' | OG1 | THR- 223 | 2.98 | 164.56 | H-Bond (Ligand Donor) |
| N3 | OG1 | THR- 223 | 2.99 | 152.93 | H-Bond (Protein Donor) |
