sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-06-11
| Name: | Lumazine protein |
|---|---|
| ID: | C4TPG1_9GAMM |
| AC: | C4TPG1 |
| Organism: | Photobacterium kishitanii |
| Reign: | Bacteria |
| TaxID: | 318456 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 83 % |
| B | 17 % |
| B-Factor: | 17.360 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.636 | 729.000 |
| % Hydrophobic | % Polar |
|---|---|
| 32.41 | 67.59 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 62.73 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -16.5416 | -4.56289 | 18.908 |
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 |
| O3' | OD2 | ASP- 31 | 2.7 | 155.06 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 31 | 3.96 | 0 | Hydrophobic |
| C7M | CG1 | VAL- 41 | 3.51 | 0 | Hydrophobic |
| C2' | SG | CYS- 47 | 4 | 0 | Hydrophobic |
| C4' | SG | CYS- 47 | 3.83 | 0 | Hydrophobic |
| O2' | O | SER- 48 | 2.71 | 164.49 | H-Bond (Ligand Donor) |
| C9 | CB | SER- 48 | 3.96 | 0 | Hydrophobic |
| O4 | N | THR- 50 | 2.92 | 158.15 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 50 | 2.99 | 146.81 | H-Bond (Protein Donor) |
| N3 | O | ASP- 62 | 2.78 | 173.47 | H-Bond (Ligand Donor) |
| O2 | N | ASP- 64 | 2.79 | 172.73 | H-Bond (Protein Donor) |
| C1' | CG | GLN- 65 | 4.01 | 0 | Hydrophobic |
| O2 | N | ALA- 66 | 2.91 | 167.86 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 66 | 3.88 | 0 | Hydrophobic |
| C5' | CB | THR- 69 | 4.37 | 0 | Hydrophobic |
| O4' | N | ILE- 102 | 3.03 | 164.83 | H-Bond (Protein Donor) |
| C5' | CB | ILE- 102 | 4.46 | 0 | Hydrophobic |
| O5' | O | ILE- 102 | 2.7 | 173.62 | H-Bond (Ligand Donor) |
| C8M | CG2 | THR- 166 | 3.99 | 0 | Hydrophobic |
| O4 | O | HOH- 196 | 2.73 | 179.96 | H-Bond (Protein Donor) |
