sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2010-08-17
| 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 | 31 % |
| C | 46 % |
| D | 23 % |
| B-Factor: | 28.726 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.963 | 1225.125 |
| % Hydrophobic | % Polar |
|---|---|
| 35.54 | 64.46 |
| According to VolSite | |
| HET Code: | H1S |
|---|---|
| Formula: | C12H15NO19S3 |
| Molecular weight: | 573.438 g/mol |
| DrugBank ID: | DB02322 |
| Buried Surface Area: | 63.99 % |
| Polar Surface area: | 355.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 19 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -17.204 | -19.7453 | -23.8086 |
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 |
| O34 | NE1 | TRP- 66 | 3.12 | 174.83 | H-Bond (Protein Donor) |
| O11 | NZ | LYS- 90 | 3.47 | 133.11 | H-Bond (Protein Donor) |
| O22 | NZ | LYS- 90 | 3.33 | 160.97 | H-Bond (Protein Donor) |
| O22 | NZ | LYS- 90 | 3.33 | 0 | Ionic (Protein Cationic) |
| C4 | CB | ALA- 92 | 4.47 | 0 | Hydrophobic |
| O29 | N | GLY- 95 | 2.93 | 146.23 | H-Bond (Protein Donor) |
| C8 | CG | PRO- 96 | 3.52 | 0 | Hydrophobic |
| O32 | OG1 | THR- 97 | 2.63 | 141.81 | H-Bond (Protein Donor) |
| O15 | ND2 | ASN- 99 | 2.78 | 148.38 | H-Bond (Protein Donor) |
| O29 | ND2 | ASN- 99 | 3.31 | 149.19 | H-Bond (Protein Donor) |
| C17 | CB | ASN- 140 | 4.32 | 0 | Hydrophobic |
| O25 | ND2 | ASN- 140 | 3.09 | 125.61 | H-Bond (Protein Donor) |
| O30 | NE2 | GLN- 150 | 3.2 | 163.89 | H-Bond (Protein Donor) |
| O32 | CZ | ARG- 170 | 3.88 | 0 | Ionic (Protein Cationic) |
| O33 | CZ | ARG- 170 | 3.29 | 0 | Ionic (Protein Cationic) |
