sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2009-07-02
| Name: | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 |
|---|---|
| ID: | DNPH1_RAT |
| AC: | O35820 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| B | 86 % |
| B-Factor: | 38.720 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.020 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.86 | 57.14 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 79.66 % |
| 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 |
|---|---|---|
| -6.91604 | 7.46617 | 6.84946 |
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 |
| N2 | OH | TYR- 13 | 2.94 | 145.26 | H-Bond (Ligand Donor) |
| O3' | N | GLY- 16 | 3.2 | 136.95 | H-Bond (Protein Donor) |
| O1P | OG | SER- 17 | 3.36 | 139.84 | H-Bond (Protein Donor) |
| O3P | OG | SER- 17 | 2.8 | 148.39 | H-Bond (Protein Donor) |
| O3P | N | ILE- 18 | 2.66 | 124.91 | H-Bond (Protein Donor) |
| C5' | CD1 | ILE- 18 | 4.19 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 18 | 4.45 | 0 | Hydrophobic |
| O3P | N | ARG- 19 | 2.89 | 138.29 | H-Bond (Protein Donor) |
| O2' | OH | TYR- 28 | 3.14 | 150.17 | H-Bond (Ligand Donor) |
| C2' | CG2 | THR- 43 | 4.26 | 0 | Hydrophobic |
| O2' | NE2 | HIS- 45 | 2.81 | 144.49 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 45 | 3.52 | 0 | Aromatic Face/Face |
| C4' | CG2 | VAL- 90 | 4.48 | 0 | Hydrophobic |
| O3' | OE1 | GLU- 93 | 2.74 | 140.67 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 93 | 2.96 | 150.66 | H-Bond (Ligand Donor) |
| O2P | N | ALA- 118 | 3.12 | 129.48 | H-Bond (Protein Donor) |
| C1' | SD | MET- 119 | 3.95 | 0 | Hydrophobic |
