sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2003-02-05
| Name: | Modification methylase RsrI |
|---|---|
| ID: | MTR1_RHOSH |
| AC: | P14751 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 1063 |
| EC Number: | 2.1.1.72 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.294 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.224 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.74 | 54.26 |
| According to VolSite | |
| HET Code: | SFG |
|---|---|
| Formula: | C15H24N7O5 |
| Molecular weight: | 382.395 g/mol |
| DrugBank ID: | DB01910 |
| Buried Surface Area: | 54.81 % |
| Polar Surface area: | 214.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 29.1289 | 23.8957 | -3.01667 |
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 | OD2 | ASP- 46 | 2.91 | 143.76 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 47 | 2.95 | 148.38 | H-Bond (Protein Donor) |
| N | OD1 | ASP- 65 | 2.62 | 158.59 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 65 | 2.62 | 0 | Ionic (Ligand Cationic) |
| N | O | PRO- 66 | 2.7 | 150.35 | H-Bond (Ligand Donor) |
| C5' | CB | PRO- 67 | 4.16 | 0 | Hydrophobic |
| O3' | NE2 | HIS- 223 | 3.03 | 160.35 | H-Bond (Protein Donor) |
| CB | CB | THR- 225 | 3.88 | 0 | Hydrophobic |
| NE | OG1 | THR- 225 | 3.15 | 160.83 | H-Bond (Ligand Donor) |
| C4' | CB | PHE- 250 | 4.29 | 0 | Hydrophobic |
| C1' | CD1 | PHE- 250 | 4.23 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 271 | 2.62 | 130.19 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 271 | 2.68 | 159.83 | H-Bond (Ligand Donor) |
| N3 | N | ALA- 272 | 3.27 | 146.25 | H-Bond (Protein Donor) |
