sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-10-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 2 |
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | PNPH_HUMAN |
| AC: | P00491 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| S | 3 % |
| T | 97 % |
| B-Factor: | 44.158 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.471 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.90 | 56.10 |
| According to VolSite | |
| HET Code: | 229 |
|---|---|
| Formula: | C11H17N4O4 |
| Molecular weight: | 269.277 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 83.13 % |
| Polar Surface area: | 134.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 38.8736 | 21.8287 | -34.9322 |
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 | CE1 | TYR- 88 | 4.26 | 0 | Hydrophobic |
| C3 | CE1 | TYR- 88 | 3.95 | 0 | Hydrophobic |
| O3 | OH | TYR- 88 | 3.08 | 128.32 | H-Bond (Protein Donor) |
| C11 | CD1 | PHE- 159 | 3.61 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 159 | 3.46 | 0 | Hydrophobic |
| C11 | CZ | PHE- 200 | 3.93 | 0 | Hydrophobic |
| N3 | OE1 | GLU- 201 | 2.95 | 120.37 | H-Bond (Ligand Donor) |
| N3 | OE2 | GLU- 201 | 2.94 | 176.52 | H-Bond (Ligand Donor) |
| C6 | SD | MET- 219 | 4 | 0 | Hydrophobic |
| C3 | CB | MET- 219 | 3.74 | 0 | Hydrophobic |
| O2 | N | MET- 219 | 2.79 | 132.3 | H-Bond (Protein Donor) |
| N1 | OD1 | ASN- 243 | 2.7 | 162.64 | H-Bond (Ligand Donor) |
| O1 | ND2 | ASN- 243 | 3.23 | 168.9 | H-Bond (Protein Donor) |
| O4 | ND1 | HIS- 257 | 2.78 | 163.77 | H-Bond (Ligand Donor) |
