sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2008-07-08
| Name: | GMP synthase [glutamine-hydrolyzing] |
|---|---|
| ID: | GUAA_HUMAN |
| AC: | P49915 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 6.3.5.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| B | 97 % |
| B-Factor: | 33.279 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.397 | 2176.875 |
| % Hydrophobic | % Polar |
|---|---|
| 47.44 | 52.56 |
| According to VolSite | |
| HET Code: | XMP |
|---|---|
| Formula: | C10H11N4O9P |
| Molecular weight: | 362.190 g/mol |
| DrugBank ID: | DB02309 |
| Buried Surface Area: | 68.99 % |
| Polar Surface area: | 207.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| 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 |
|---|---|---|
| -0.314333 | -8.23771 | -19.8796 |
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 |
| O6 | NE | ARG- 337 | 2.79 | 156.01 | H-Bond (Protein Donor) |
| N7 | NH2 | ARG- 337 | 3.01 | 164.92 | H-Bond (Protein Donor) |
| C1' | CB | PRO- 439 | 4.36 | 0 | Hydrophobic |
| O2 | N | GLY- 440 | 2.93 | 157.26 | H-Bond (Protein Donor) |
| O2' | NE2 | GLN- 610 | 2.72 | 151.15 | H-Bond (Protein Donor) |
| O3' | OE1 | GLN- 610 | 2.5 | 167.51 | H-Bond (Ligand Donor) |
| C5' | CB | PHE- 645 | 4.24 | 0 | Hydrophobic |
| C3' | CD1 | PHE- 645 | 3.95 | 0 | Hydrophobic |
| O1P | NZ | LYS- 685 | 3.7 | 0 | Ionic (Protein Cationic) |
| O2P | NZ | LYS- 685 | 2.94 | 0 | Ionic (Protein Cationic) |
| O2P | NZ | LYS- 685 | 2.94 | 171.89 | H-Bond (Protein Donor) |
| O2P | OG1 | THR- 690 | 2.7 | 147.32 | H-Bond (Protein Donor) |
| O2P | N | THR- 690 | 2.72 | 170.98 | H-Bond (Protein Donor) |
| O5' | OG1 | THR- 690 | 3.16 | 131.39 | H-Bond (Protein Donor) |
| C5' | CB | THR- 690 | 4.24 | 0 | Hydrophobic |
| C3' | CB | THR- 690 | 3.98 | 0 | Hydrophobic |
| O3P | N | GLU- 691 | 2.99 | 163.39 | H-Bond (Protein Donor) |
| C2' | CG | GLU- 691 | 3.6 | 0 | Hydrophobic |
| O2' | OE1 | GLU- 691 | 2.58 | 165.8 | H-Bond (Ligand Donor) |
