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
2005-07-13
| Name: | GMP reductase 1 |
|---|---|
| ID: | GMPR1_HUMAN |
| AC: | P36959 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 18.449 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.068 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 56.25 | 43.75 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 78.77 % |
| Polar Surface area: | 217.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -7.02304 | 24.7708 | -83.8075 |
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 |
| C5' | CB | ALA- 53 | 4.39 | 0 | Hydrophobic |
| C3' | CB | ALA- 53 | 3.99 | 0 | Hydrophobic |
| C3' | SD | MET- 55 | 3.98 | 0 | Hydrophobic |
| O1P | N | SER- 184 | 2.62 | 158.13 | H-Bond (Protein Donor) |
| O3P | N | SER- 184 | 3.47 | 134.05 | H-Bond (Protein Donor) |
| O3P | OG | SER- 184 | 2.61 | 153.48 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 219 | 3.49 | 124.87 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 219 | 2.5 | 155.83 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 219 | 2.74 | 124.61 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 219 | 3.45 | 142.7 | H-Bond (Ligand Donor) |
| O1P | N | GLY- 221 | 3.13 | 174.22 | H-Bond (Protein Donor) |
| O2P | N | GLY- 242 | 2.92 | 165.14 | H-Bond (Protein Donor) |
| O2P | N | GLY- 243 | 3.15 | 153.72 | H-Bond (Protein Donor) |
| O3P | N | GLY- 243 | 3.16 | 138.18 | H-Bond (Protein Donor) |
| N7 | N | MET- 269 | 2.97 | 169.1 | H-Bond (Protein Donor) |
| C2' | SD | MET- 269 | 3.94 | 0 | Hydrophobic |
| O6 | N | SER- 270 | 3.26 | 161.32 | H-Bond (Protein Donor) |
| C2' | CD | ARG- 286 | 4.07 | 0 | Hydrophobic |
| O2' | NH1 | ARG- 286 | 3.1 | 125.58 | H-Bond (Protein Donor) |
| N1 | OG | SER- 288 | 3.12 | 132.01 | H-Bond (Protein Donor) |
| N2 | OG | SER- 288 | 2.8 | 124.65 | H-Bond (Ligand Donor) |
| O3' | O | HOH- 2033 | 2.79 | 172.29 | H-Bond (Protein Donor) |
| O2P | O | HOH- 2037 | 3.18 | 179.99 | H-Bond (Protein Donor) |
