sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2014-05-01
| Name: | Peptidoglycan recognition protein 1 |
|---|---|
| ID: | PGRP1_CAMDR |
| AC: | Q9GK12 |
| Organism: | Camelus dromedarius |
| Reign: | Eukaryota |
| TaxID: | 9838 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 40 % |
| D | 60 % |
| B-Factor: | 52.587 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.036 | 1589.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.80 | 55.20 |
| According to VolSite | |
| HET Code: | XXH |
|---|---|
| Formula: | C7H5NO3 |
| Molecular weight: | 151.119 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.54 % |
| Polar Surface area: | 62.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -20.0949 | -28.8844 | -17.6405 |
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 |
| C6 | CB | ALA- 92 | 3.75 | 0 | Hydrophobic |
| O3 | N | GLY- 95 | 3.18 | 147.85 | H-Bond (Protein Donor) |
| C7 | CG | PRO- 96 | 4.42 | 0 | Hydrophobic |
| C2 | CG | PRO- 96 | 4.41 | 0 | Hydrophobic |
