sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2003-05-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.480 | 9.620 | 10.240 | 0.810 | 10.250 | 11 |
| 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 |
|---|---|
| E | 100 % |
| B-Factor: | 28.968 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.096 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 48.69 | 51.31 |
| According to VolSite | |
| HET Code: | IMH |
|---|---|
| Formula: | C11H15N4O4 |
| Molecular weight: | 267.261 g/mol |
| DrugBank ID: | DB06185 |
| Buried Surface Area: | 72.04 % |
| Polar Surface area: | 139.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 52.7764 | 47.1651 | 29.0425 |
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 |
| C5' | CB | SER- 33 | 4.37 | 0 | Hydrophobic |
| C3' | CE1 | TYR- 88 | 4.42 | 0 | Hydrophobic |
| O3' | OH | TYR- 88 | 3.03 | 156.19 | H-Bond (Protein Donor) |
| N1 | OE1 | GLU- 201 | 3.15 | 124.5 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 201 | 2.52 | 153.04 | H-Bond (Ligand Donor) |
| C2' | SD | MET- 219 | 3.95 | 0 | Hydrophobic |
| O2' | N | MET- 219 | 3.16 | 130.31 | H-Bond (Protein Donor) |
| N7 | OD1 | ASN- 243 | 2.9 | 154.7 | H-Bond (Ligand Donor) |
| O6 | ND2 | ASN- 243 | 3.45 | 137.52 | H-Bond (Protein Donor) |
| O5' | CD2 | HIS- 257 | 2.77 | 156.96 | Weak HBond LIG |
| C5' | CB | HIS- 257 | 4.38 | 0 | Hydrophobic |
