sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.090 Å
X-ray
2005-12-07
| Name: | Phosphoenolpyruvate carboxykinase [GTP], mitochondrial |
|---|---|
| ID: | PCKGM_CHICK |
| AC: | P21642 |
| Organism: | Gallus gallus |
| Reign: | Eukaryota |
| TaxID: | 9031 |
| EC Number: | 4.1.1.32 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.078 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MN MN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.169 | 391.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.97 | 56.03 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 68.3 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 12.1731 | 54.7722 | 7.12271 |
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 |
| O1B | N | ALA- 306 | 2.87 | 141.84 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 306 | 4.1 | 0 | Hydrophobic |
| O3B | N | CYS- 307 | 3.24 | 139.63 | H-Bond (Protein Donor) |
| O3B | N | GLY- 308 | 3.13 | 129.84 | H-Bond (Protein Donor) |
| O3A | N | GLY- 308 | 2.97 | 147.14 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 309 | 2.83 | 151.36 | H-Bond (Protein Donor) |
| O3B | N | LYS- 309 | 2.92 | 158.11 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 309 | 2.83 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 310 | 2.72 | 153.63 | H-Bond (Protein Donor) |
| O1A | N | ASN- 311 | 2.88 | 169.64 | H-Bond (Protein Donor) |
| O1A | ND2 | ASN- 311 | 2.64 | 164.73 | H-Bond (Protein Donor) |
| C5' | CB | VAL- 354 | 4.25 | 0 | Hydrophobic |
| C3' | CG1 | VAL- 354 | 4.14 | 0 | Hydrophobic |
| O3' | O | PRO- 356 | 2.77 | 168.23 | H-Bond (Ligand Donor) |
| O6 | N | PHE- 549 | 3.02 | 170.21 | H-Bond (Protein Donor) |
| C2' | CE1 | PHE- 549 | 4.16 | 0 | Hydrophobic |
| O6 | ND2 | ASN- 552 | 3.03 | 152.34 | H-Bond (Protein Donor) |
| O2A | MN | MN- 2003 | 2.64 | 0 | Metal Acceptor |
| O1B | O | HOH- 2141 | 2.82 | 179.95 | H-Bond (Protein Donor) |
| N3 | O | HOH- 2246 | 3.04 | 179.96 | H-Bond (Protein Donor) |
