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
2006-10-17
| Name: | 5,6-dimethylbenzimidazole synthase |
|---|---|
| ID: | BLUB_RHIME |
| AC: | Q92PC8 |
| Organism: | Rhizobium meliloti |
| Reign: | Bacteria |
| TaxID: | 266834 |
| EC Number: | 1.13.11.79 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 42 % |
| H | 57 % |
| B-Factor: | 17.633 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.428 | 351.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.92 | 48.08 |
| According to VolSite | |
| HET Code: | FNR |
|---|---|
| Formula: | C17H21N4O9P |
| Molecular weight: | 456.344 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.01 % |
| Polar Surface area: | 216.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.0742 | -35.7025 | 53.9095 |
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 |
| O3P | NH2 | ARG- 30 | 2.62 | 124.07 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 30 | 2.87 | 0 | Ionic (Protein Cationic) |
| O1P | NE | ARG- 31 | 3.04 | 130.88 | H-Bond (Protein Donor) |
| O2P | NE | ARG- 31 | 2.61 | 142.34 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 31 | 3.18 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 31 | 3.64 | 0 | Ionic (Protein Cationic) |
| C1' | CB | ASP- 32 | 3.84 | 0 | Hydrophobic |
| C3' | CB | ASP- 32 | 3.94 | 0 | Hydrophobic |
| O2P | N | ASP- 32 | 2.77 | 159.31 | H-Bond (Protein Donor) |
| N1 | NH2 | ARG- 34 | 3.2 | 145.57 | H-Bond (Protein Donor) |
| O2 | NE | ARG- 34 | 2.6 | 162.08 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 34 | 3.26 | 127.25 | H-Bond (Protein Donor) |
| C8M | CG | PRO- 58 | 4 | 0 | Hydrophobic |
| C9 | CB | PRO- 58 | 4.5 | 0 | Hydrophobic |
| C6 | CB | VAL- 60 | 3.72 | 0 | Hydrophobic |
| C8 | CB | VAL- 60 | 4.07 | 0 | Hydrophobic |
| C4' | CD1 | PHE- 62 | 4.12 | 0 | Hydrophobic |
| N3 | O | LEU- 108 | 2.97 | 139.71 | H-Bond (Ligand Donor) |
| C7M | SD | MET- 140 | 3.29 | 0 | Hydrophobic |
| C7M | CB | TYR- 143 | 3.95 | 0 | Hydrophobic |
| C8M | CB | SER- 144 | 4.06 | 0 | Hydrophobic |
| C8M | SG | CYS- 147 | 4.35 | 0 | Hydrophobic |
| C6 | CB | TRP- 165 | 4.27 | 0 | Hydrophobic |
| C7M | CZ2 | TRP- 165 | 3.64 | 0 | Hydrophobic |
| C8M | CE3 | TRP- 165 | 4.28 | 0 | Hydrophobic |
| C9A | CB | TRP- 165 | 3.89 | 0 | Hydrophobic |
| O4 | N | SER- 167 | 2.84 | 167.3 | H-Bond (Protein Donor) |
| C6 | CB | SER- 167 | 4.07 | 0 | Hydrophobic |
| C5' | CB | PRO- 202 | 4.2 | 0 | Hydrophobic |
| O1P | O | HOH- 578 | 3.34 | 179.96 | H-Bond (Protein Donor) |
