sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2011-02-03
| Name: | Phosphoribosyl isomerase A |
|---|---|
| ID: | HIS4_MYCTU |
| AC: | P9WMM5 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 5.3.1.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 23.461 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.001 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 35.81 | 64.19 |
| According to VolSite | |
| HET Code: | 137 |
|---|---|
| Formula: | C12H15NO9P |
| Molecular weight: | 348.223 g/mol |
| DrugBank ID: | DB03543 |
| Buried Surface Area: | 68.25 % |
| Polar Surface area: | 195.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 7.1477 | -2.19943 | 39.1184 |
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- 11 | 3.29 | 170.78 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 11 | 2.71 | 160.69 | H-Bond (Ligand Donor) |
| O71 | NE2 | HIS- 50 | 3.05 | 165.3 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 52 | 4.3 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 52 | 3.66 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 54 | 3.76 | 0 | Hydrophobic |
| C5 | CB | ALA- 57 | 3.88 | 0 | Hydrophobic |
| O71 | OG | SER- 81 | 3.19 | 148.25 | H-Bond (Protein Donor) |
| O72 | OG | SER- 81 | 2.52 | 145.72 | H-Bond (Protein Donor) |
| DuAr | CZ | ARG- 143 | 3.86 | 22.92 | Pi/Cation |
| C3 | CD | ARG- 143 | 3.94 | 0 | Hydrophobic |
| C5 | CB | ARG- 143 | 3.58 | 0 | Hydrophobic |
| O4' | OD1 | ASP- 175 | 2.75 | 150.9 | H-Bond (Ligand Donor) |
| O2P | N | GLY- 176 | 2.83 | 146 | H-Bond (Protein Donor) |
| O4' | OG | SER- 200 | 2.79 | 136.93 | H-Bond (Protein Donor) |
| O2P | N | GLY- 202 | 2.76 | 158.83 | H-Bond (Protein Donor) |
| C4' | CG2 | ILE- 224 | 3.93 | 0 | Hydrophobic |
| O1P | N | GLY- 226 | 2.84 | 176.29 | H-Bond (Protein Donor) |
| O3P | N | LYS- 227 | 2.83 | 172.22 | H-Bond (Protein Donor) |
