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
2009-06-12
| 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 | 88 % |
| B | 12 % |
| B-Factor: | 12.633 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.136 | 1174.500 |
| % Hydrophobic | % Polar |
|---|---|
| 32.47 | 67.53 |
| According to VolSite | |
| HET Code: | DLZ |
|---|---|
| Formula: | C13H18N4O6 |
| Molecular weight: | 326.305 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.89 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 16.0554 | -3.86187 | -18.872 |
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 | 2.66 | 156.34 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 31 | 3.85 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 41 | 3.64 | 0 | Hydrophobic |
| C2' | SG | CYS- 47 | 4.02 | 0 | Hydrophobic |
| C4' | SG | CYS- 47 | 3.84 | 0 | Hydrophobic |
| C7 | CB | SER- 48 | 4.1 | 0 | Hydrophobic |
| O2' | O | SER- 48 | 2.7 | 160.65 | H-Bond (Ligand Donor) |
| N5 | OG1 | THR- 50 | 3.01 | 150.37 | H-Bond (Protein Donor) |
| O4 | N | THR- 50 | 2.85 | 162.24 | H-Bond (Protein Donor) |
| N3 | O | ASP- 62 | 2.75 | 173.15 | H-Bond (Ligand Donor) |
| O2 | N | ASP- 64 | 2.86 | 169.59 | H-Bond (Protein Donor) |
| C1' | CG | GLN- 65 | 4.15 | 0 | Hydrophobic |
| O2 | N | ALA- 66 | 2.9 | 163.12 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 66 | 3.78 | 0 | Hydrophobic |
| C5' | CB | THR- 69 | 4.38 | 0 | Hydrophobic |
| O5' | OG1 | THR- 69 | 2.57 | 166.29 | H-Bond (Protein Donor) |
| O4' | N | ILE- 102 | 2.87 | 170.08 | H-Bond (Protein Donor) |
| C5' | CB | ILE- 102 | 4.45 | 0 | Hydrophobic |
| O5' | O | ILE- 102 | 2.67 | 176.5 | H-Bond (Ligand Donor) |
