sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2013-04-28
| Name: | Diguanylate cyclase |
|---|---|
| ID: | B0RM05_XANCB |
| AC: | B0RM05 |
| Organism: | Xanthomonas campestris pv. campestris |
| Reign: | Bacteria |
| TaxID: | 509169 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 58.254 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.042 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.88 | 38.12 |
| According to VolSite | |
| HET Code: | PCG |
|---|---|
| Formula: | C10H11N5O7P |
| Molecular weight: | 344.197 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.3 % |
| Polar Surface area: | 183.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -18.9989 | 24.1333 | -10.2369 |
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' | CE1 | PHE- 51 | 3.95 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 70 | 3.75 | 0 | Hydrophobic |
| C1' | CZ | PHE- 72 | 4.31 | 0 | Hydrophobic |
| C4' | CB | PHE- 87 | 4.27 | 0 | Hydrophobic |
| C1' | CB | PHE- 87 | 4 | 0 | Hydrophobic |
| O3' | N | GLY- 88 | 3.42 | 131.09 | H-Bond (Protein Donor) |
| O2' | N | GLY- 88 | 2.88 | 149.68 | H-Bond (Protein Donor) |
| O2' | OE2 | GLU- 89 | 3.34 | 170.74 | H-Bond (Ligand Donor) |
| C3' | CD1 | LEU- 90 | 3.23 | 0 | Hydrophobic |
| O2A | NE2 | HIS- 97 | 3.13 | 142.52 | H-Bond (Ligand Donor) |
| C5' | CB | ARG- 99 | 4.46 | 0 | Hydrophobic |
| O2A | N | SER- 100 | 2.83 | 170.36 | H-Bond (Protein Donor) |
| N2 | OG | SER- 100 | 3.34 | 129.45 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 101 | 4.37 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 145 | 2.74 | 126.82 | H-Bond (Ligand Donor) |
