sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.360 Å
X-ray
2010-05-19
| Name: | Protein NrdI |
|---|---|
| ID: | NRDI_ECOLI |
| AC: | P0A772 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 19 % |
| D | 81 % |
| B-Factor: | 36.623 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.099 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.37 | 44.63 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 80.17 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -33.2326 | -58.3002 | 15.9566 |
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 | OG | SER- 8 | 2.71 | 162.25 | H-Bond (Protein Donor) |
| O2P | N | SER- 9 | 3.03 | 158.62 | H-Bond (Protein Donor) |
| O2P | OG | SER- 9 | 3.11 | 139.4 | H-Bond (Protein Donor) |
| O1P | OG | SER- 11 | 2.64 | 146.17 | H-Bond (Protein Donor) |
| O1P | N | ASN- 13 | 2.82 | 167.38 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 13 | 3.99 | 0 | Hydrophobic |
| O3P | N | THR- 14 | 2.86 | 165.98 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 14 | 2.77 | 152.91 | H-Bond (Protein Donor) |
| C7M | CG | GLU- 21 | 4.14 | 0 | Hydrophobic |
| C6 | CD | ARG- 25 | 4.1 | 0 | Hydrophobic |
| C7 | CG | ARG- 25 | 4.27 | 0 | Hydrophobic |
| C7M | CB | ARG- 25 | 3.72 | 0 | Hydrophobic |
| C5' | CB | PRO- 47 | 3.95 | 0 | Hydrophobic |
| O2' | N | SER- 48 | 3.31 | 134.97 | H-Bond (Protein Donor) |
| O2' | O | SER- 48 | 2.75 | 159.43 | H-Bond (Ligand Donor) |
| C6 | CB | TYR- 49 | 4.43 | 0 | Hydrophobic |
| C7M | CD1 | TYR- 49 | 4.1 | 0 | Hydrophobic |
| C8M | CE1 | TYR- 49 | 3.61 | 0 | Hydrophobic |
| C5' | CZ | TYR- 49 | 4.13 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 49 | 3.5 | 0 | Hydrophobic |
| O2P | OH | TYR- 49 | 2.57 | 175.1 | H-Bond (Protein Donor) |
| N5 | N | GLY- 50 | 3.35 | 123.42 | H-Bond (Protein Donor) |
| O4' | OG | SER- 81 | 3.34 | 172.93 | H-Bond (Ligand Donor) |
| O2 | N | ASN- 83 | 2.97 | 165.3 | H-Bond (Protein Donor) |
| C1' | CE2 | PHE- 86 | 3.68 | 0 | Hydrophobic |
| N3 | O | ALA- 89 | 2.63 | 176.71 | H-Bond (Ligand Donor) |
| O2 | N | GLY- 91 | 3.04 | 166.16 | H-Bond (Protein Donor) |
| C3' | CD2 | LEU- 111 | 4.44 | 0 | Hydrophobic |
| C8M | CE2 | TYR- 197 | 3.49 | 0 | Hydrophobic |
