sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-07-09
| 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 |
|---|---|
| A | 14 % |
| C | 44 % |
| D | 42 % |
| B-Factor: | 38.496 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.073 | 1299.375 |
| % Hydrophobic | % Polar |
|---|---|
| 36.10 | 63.90 |
| According to VolSite | |
| HET Code: | MU2 |
|---|---|
| Formula: | C19H31N4O11 |
| Molecular weight: | 491.470 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.53 % |
| Polar Surface area: | 249.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 7 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -12.6447 | -21.611 | -23.215 |
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 |
| C8 | CH2 | TRP- 66 | 4.12 | 0 | Hydrophobic |
| C3 | CZ2 | TRP- 66 | 3.52 | 0 | Hydrophobic |
| C18 | CZ2 | TRP- 66 | 4.43 | 0 | Hydrophobic |
| O18 | NE1 | TRP- 66 | 2.7 | 145.4 | H-Bond (Protein Donor) |
| C1 | CB | ALA- 92 | 4.32 | 0 | Hydrophobic |
| C5 | CB | ALA- 92 | 3.93 | 0 | Hydrophobic |
| C1 | CG | PRO- 96 | 4.26 | 0 | Hydrophobic |
| C4 | CG | PRO- 96 | 3.6 | 0 | Hydrophobic |
| C20 | CG | PRO- 96 | 4.04 | 0 | Hydrophobic |
| N4 | OG1 | THR- 97 | 3.26 | 159.7 | H-Bond (Ligand Donor) |
| C23 | CG2 | THR- 97 | 4.04 | 0 | Hydrophobic |
| C20 | CB | THR- 97 | 3.67 | 0 | Hydrophobic |
| C25 | CZ2 | TRP- 98 | 3.36 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 99 | 2.57 | 135.7 | H-Bond (Protein Donor) |
| C23 | CB | ASN- 140 | 3.55 | 0 | Hydrophobic |
| C25 | CB | ASN- 140 | 4.45 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 150 | 2.88 | 165.93 | H-Bond (Protein Donor) |
| C8 | CG | PRO- 151 | 4.02 | 0 | Hydrophobic |
