sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-12-23
| Name: | GTP-binding nuclear protein GSP1/CNR1 |
|---|---|
| ID: | GSP1_YEAST |
| AC: | P32835 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 51.219 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.047 | 1532.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.59 | 54.41 |
| According to VolSite | |
| HET Code: | GTP |
|---|---|
| Formula: | C10H12N5O14P3 |
| Molecular weight: | 519.149 g/mol |
| DrugBank ID: | DB04137 |
| Buried Surface Area: | 79.38 % |
| Polar Surface area: | 335.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -55.8803 | 20.4762 | 8.36031 |
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 |
| O3B | N | GLY- 22 | 2.79 | 160.26 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 25 | 2.6 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 25 | 3.12 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 25 | 3.12 | 168.72 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 27 | 2.61 | 121.15 | H-Bond (Protein Donor) |
| O1A | N | THR- 27 | 3.22 | 159.31 | H-Bond (Protein Donor) |
| C5' | CB | THR- 27 | 4.12 | 0 | Hydrophobic |
| C3' | CG2 | THR- 27 | 4.38 | 0 | Hydrophobic |
| C2' | CZ | PHE- 37 | 3.4 | 0 | Hydrophobic |
| O3' | O | GLU- 38 | 3.19 | 130.15 | H-Bond (Ligand Donor) |
| C4' | CB | TYR- 41 | 4.17 | 0 | Hydrophobic |
| O3G | N | THR- 44 | 2.65 | 137.91 | H-Bond (Protein Donor) |
| O1G | N | GLY- 70 | 3.24 | 151.39 | H-Bond (Protein Donor) |
| O2G | N | GLY- 70 | 3.04 | 128.43 | H-Bond (Protein Donor) |
| O2G | N | LEU- 71 | 3.34 | 134.07 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 124 | 3.05 | 131.94 | H-Bond (Protein Donor) |
| O6 | N | LYS- 125 | 3.43 | 123.22 | H-Bond (Protein Donor) |
| N1 | OD2 | ASP- 127 | 3.46 | 131.37 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 127 | 2.63 | 171.27 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 127 | 3.24 | 137.33 | H-Bond (Ligand Donor) |
| O6 | OG | SER- 152 | 3.39 | 162.89 | H-Bond (Protein Donor) |
| O6 | N | LYS- 154 | 3.13 | 148.53 | H-Bond (Protein Donor) |
| O3G | MG | MG- 1182 | 2.65 | 0 | Metal Acceptor |
| O2B | MG | MG- 1182 | 2.28 | 0 | Metal Acceptor |
| O2G | O | HOH- 2015 | 2.83 | 151 | H-Bond (Protein Donor) |
