sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.180 Å
X-ray
2013-06-13
| Name: | Phosphoribosylformylglycinamidine synthase |
|---|---|
| ID: | PUR4_SALTY |
| AC: | P74881 |
| Organism: | Salmonella typhimurium |
| Reign: | Bacteria |
| TaxID: | 99287 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.604 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.402 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.18 | 57.82 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.46 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -24.7736 | 40.4887 | 8.07081 |
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 |
| O2' | N | GLY- 387 | 2.99 | 139.35 | H-Bond (Protein Donor) |
| N6 | O | TYR- 388 | 3.05 | 142.13 | H-Bond (Ligand Donor) |
| O2A | NZ | LYS- 649 | 3.83 | 0 | Ionic (Protein Cationic) |
| C5' | CG | LYS- 649 | 3.9 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 653 | 4.31 | 0 | Hydrophobic |
| N3 | NE2 | GLN- 668 | 3.41 | 163.29 | H-Bond (Protein Donor) |
| C1' | CG | GLN- 668 | 3.74 | 0 | Hydrophobic |
| O3' | O | ALA- 678 | 2.6 | 162.67 | H-Bond (Ligand Donor) |
| O1B | ND2 | ASN- 722 | 3.2 | 168.3 | H-Bond (Protein Donor) |
| O3B | OG | SER- 886 | 3.1 | 138.73 | H-Bond (Protein Donor) |
| O2B | MG | MG- 1302 | 1.96 | 0 | Metal Acceptor |
| O1B | MG | MG- 1303 | 2.13 | 0 | Metal Acceptor |
| O3B | MG | MG- 1304 | 2.06 | 0 | Metal Acceptor |
| O2A | MG | MG- 1304 | 2.06 | 0 | Metal Acceptor |
