sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
0.950 Å
X-ray
2012-04-01
| Name: | Putative histidine triad (HIT) protein |
|---|---|
| ID: | Q182D4_PEPD6 |
| AC: | Q182D4 |
| Organism: | Peptoclostridium difficile |
| Reign: | Bacteria |
| TaxID: | 272563 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| B | 96 % |
| B-Factor: | 12.869 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | K |
| Ligandability | Volume (Å3) |
|---|---|
| 0.023 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.18 | 58.82 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.88 % |
| Polar Surface area: | 217.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -17.3677 | 0.234583 | 31.3351 |
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' | CZ | PHE- 8 | 4.39 | 0 | Hydrophobic |
| C4' | CZ | PHE- 8 | 4.25 | 0 | Hydrophobic |
| N2 | O | ASN- 31 | 2.92 | 145.56 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 32 | 2.57 | 171.7 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 32 | 3.22 | 127.7 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 32 | 2.61 | 165.56 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 33 | 3.23 | 152.12 | H-Bond (Protein Donor) |
| O2' | ND2 | ASN- 34 | 2.78 | 164.79 | H-Bond (Protein Donor) |
| C4' | CD1 | LEU- 42 | 4.15 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 42 | 4.03 | 0 | Hydrophobic |
| O3P | ND2 | ASN- 89 | 2.83 | 159.95 | H-Bond (Protein Donor) |
| O2P | N | GLU- 97 | 2.71 | 160.52 | H-Bond (Protein Donor) |
| O2P | N | VAL- 98 | 2.92 | 168.95 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 98 | 3.86 | 0 | Hydrophobic |
| O3P | NE2 | HIS- 102 | 2.75 | 179.79 | H-Bond (Protein Donor) |
| O3P | NE2 | HIS- 104 | 2.92 | 166.1 | H-Bond (Protein Donor) |
| N2 | O | HOH- 306 | 3.23 | 120.15 | H-Bond (Ligand Donor) |
