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
2011-09-21
| Name: | Pyruvate carboxylase |
|---|---|
| ID: | Q2K340_RHIEC |
| AC: | Q2K340 |
| Organism: | Rhizobium etli |
| Reign: | Bacteria |
| TaxID: | 347834 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 67.984 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.964 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.23 | 46.77 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.1 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -60.637 | -37.4974 | -0.526926 |
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 |
| C1' | CE | MET- 164 | 4.16 | 0 | Hydrophobic |
| O1A | NZ | LYS- 166 | 3.07 | 162.99 | H-Bond (Protein Donor) |
| N7 | NZ | LYS- 166 | 3.32 | 139.38 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 166 | 3.07 | 0 | Ionic (Protein Cationic) |
| C5' | SD | MET- 176 | 4.41 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 208 | 3.02 | 158.63 | H-Bond (Ligand Donor) |
| N6 | O | LYS- 209 | 3.16 | 160.89 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 211 | 3.18 | 130.33 | H-Bond (Protein Donor) |
| O3' | ND1 | HIS- 216 | 2.59 | 155.59 | H-Bond (Ligand Donor) |
| O3' | NE2 | GLN- 240 | 2.62 | 157.12 | H-Bond (Protein Donor) |
| O2' | OE1 | GLN- 240 | 2.82 | 160.66 | H-Bond (Ligand Donor) |
| C4' | CB | ASN- 243 | 4.23 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 296 | 4.45 | 0 | Hydrophobic |
| C2' | CG2 | THR- 454 | 4.36 | 0 | Hydrophobic |
| O2' | OG1 | THR- 454 | 3.45 | 126.55 | H-Bond (Protein Donor) |
| O1B | MG | MG- 2002 | 2.1 | 0 | Metal Acceptor |
| O2A | MG | MG- 2002 | 2.19 | 0 | Metal Acceptor |
