sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-05-27
| 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 | 72 % |
| B | 19 % |
| C | 8 % |
| B-Factor: | 12.758 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.116 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 62.04 | 37.96 |
| According to VolSite | |
| HET Code: | 6K6 |
|---|---|
| Formula: | C15H16N5O8P |
| Molecular weight: | 425.290 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.76 % |
| Polar Surface area: | 200.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 4.63424 | -2.85641 | 39.8293 |
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 |
| O3' | N | GLY- 16 | 3.23 | 156.63 | H-Bond (Protein Donor) |
| C3' | CG1 | ILE- 18 | 4.09 | 0 | Hydrophobic |
| C5' | CG1 | ILE- 18 | 4.18 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 18 | 4.06 | 0 | Hydrophobic |
| O3 | N | ILE- 18 | 3.07 | 158.62 | H-Bond (Protein Donor) |
| O2 | N | ARG- 19 | 2.89 | 152.51 | H-Bond (Protein Donor) |
| O3 | N | GLY- 20 | 2.93 | 139.6 | H-Bond (Protein Donor) |
| C61 | CB | HIS- 45 | 4.44 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 46 | 3.74 | 0 | Hydrophobic |
| N3 | ND2 | ASN- 69 | 2.95 | 149.92 | H-Bond (Protein Donor) |
| O3 | OG | SER- 87 | 2.52 | 146.11 | H-Bond (Protein Donor) |
| O1 | N | GLY- 89 | 3.27 | 144.26 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 90 | 4.22 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 93 | 3.49 | 141.92 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 93 | 3.43 | 123.25 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 93 | 2.76 | 157.82 | H-Bond (Ligand Donor) |
| O1 | OG | SER- 117 | 3.2 | 142.96 | H-Bond (Protein Donor) |
| C1' | CG | MET- 119 | 3.99 | 0 | Hydrophobic |
| C4' | CG | MET- 119 | 4.1 | 0 | Hydrophobic |
