sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2005-11-27
| Name: | Modification methylase HhaI |
|---|---|
| ID: | MTH1_HAEPH |
| AC: | P05102 |
| Organism: | Haemophilus parahaemolyticus |
| Reign: | Bacteria |
| TaxID: | 735 |
| EC Number: | 2.1.1.37 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 9.673 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.986 | 1154.250 |
| % Hydrophobic | % Polar |
|---|---|
| 38.01 | 61.99 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 72.99 % |
| 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 |
|---|---|---|
| -14.1793 | 28.5204 | 84.4531 |
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 |
| C1' | CD1 | PHE- 18 | 4.17 | 0 | Hydrophobic |
| C4' | CB | PHE- 18 | 3.8 | 0 | Hydrophobic |
| OXT | N | LEU- 21 | 3 | 160.34 | H-Bond (Protein Donor) |
| O | N | GLY- 23 | 3.11 | 141.03 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 40 | 2.52 | 167.73 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 40 | 3.21 | 124.3 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 40 | 2.57 | 162.18 | H-Bond (Ligand Donor) |
| N3 | N | TRP- 41 | 3.17 | 148.65 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 60 | 3.08 | 155.13 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 61 | 3.04 | 170.34 | H-Bond (Protein Donor) |
| C5' | CG | PRO- 80 | 4.4 | 0 | Hydrophobic |
| SD | CB | ASN- 304 | 3.83 | 0 | Hydrophobic |
| O | OG | SER- 305 | 2.89 | 125.85 | H-Bond (Protein Donor) |
| OXT | OG | SER- 305 | 2.77 | 171.53 | H-Bond (Protein Donor) |
| N | O | HOH- 2068 | 2.79 | 150.95 | H-Bond (Ligand Donor) |
| N | O | HOH- 2248 | 2.95 | 160.9 | H-Bond (Ligand Donor) |
