sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2010-07-04
| Name: | Cytosolic purine 5'-nucleotidase |
|---|---|
| ID: | 5NTC_HUMAN |
| AC: | P49902 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.3.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.245 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.241 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 34.73 | 65.27 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.69 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 2.92976 | 15.5668 | 41.77 |
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 |
| O2P | ND2 | ASN- 52 | 2.56 | 172 | H-Bond (Protein Donor) |
| O1P | N | MET- 53 | 3.32 | 144.42 | H-Bond (Protein Donor) |
| C5' | CB | ASP- 54 | 3.93 | 0 | Hydrophobic |
| O1P | N | ASP- 54 | 3.15 | 159.79 | H-Bond (Protein Donor) |
| C2' | CZ | PHE- 157 | 3.95 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 157 | 3.82 | 0 | Hydrophobic |
| O4 | NH2 | ARG- 202 | 2.79 | 155.37 | H-Bond (Protein Donor) |
| O2' | ND1 | HIS- 209 | 2.97 | 161.01 | H-Bond (Ligand Donor) |
| C1' | CZ | TYR- 210 | 3.96 | 0 | Hydrophobic |
| O2' | NZ | LYS- 215 | 3.43 | 166.97 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 249 | 2.58 | 158.08 | H-Bond (Protein Donor) |
| O3P | N | ASN- 250 | 2.86 | 171.37 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 250 | 4.02 | 0 | Hydrophobic |
| O3' | OG | SER- 251 | 2.73 | 169.45 | H-Bond (Ligand Donor) |
| O3P | NZ | LYS- 292 | 3.32 | 0 | Ionic (Protein Cationic) |
| O2P | MG | MG- 1493 | 2.03 | 0 | Metal Acceptor |
