sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2010-07-27
| Name: | Dehydrogenase/reductase SDR family member 4 |
|---|---|
| ID: | DHRS4_HUMAN |
| AC: | Q9BTZ2 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.184 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 29.403 |
|---|---|
| Number of residues: | 53 |
| Including | |
| Standard Amino Acids: | 50 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.290 | 1360.125 |
| % Hydrophobic | % Polar |
|---|---|
| 51.86 | 48.14 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 75.81 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 49.4347 | 10.7463 | 32.9207 |
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 |
| O2N | O | HOH- 14 | 2.58 | 174.47 | H-Bond (Protein Donor) |
| C4B | CB | ALA- 39 | 3.93 | 0 | Hydrophobic |
| C1B | CB | ALA- 39 | 3.53 | 0 | Hydrophobic |
| O3B | N | THR- 41 | 3.27 | 142.63 | H-Bond (Protein Donor) |
| O3B | OG1 | THR- 41 | 2.8 | 146.2 | H-Bond (Ligand Donor) |
| C3B | CB | ASP- 42 | 3.96 | 0 | Hydrophobic |
| O2N | N | ILE- 44 | 2.75 | 156.34 | H-Bond (Protein Donor) |
| C3N | CD1 | ILE- 44 | 4.18 | 0 | Hydrophobic |
| O2X | OG | SER- 63 | 2.59 | 167.2 | H-Bond (Protein Donor) |
| C1B | CB | SER- 63 | 4.02 | 0 | Hydrophobic |
| O1X | NH2 | ARG- 64 | 3.04 | 167.85 | H-Bond (Protein Donor) |
| O3X | NE | ARG- 64 | 2.75 | 161.99 | H-Bond (Protein Donor) |
| O3X | N | ARG- 64 | 2.83 | 156.9 | H-Bond (Protein Donor) |
| O1X | CZ | ARG- 64 | 3.84 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 64 | 3.63 | 0 | Ionic (Protein Cationic) |
| O2X | N | LYS- 65 | 3.3 | 150.72 | H-Bond (Protein Donor) |
| O2X | ND2 | ASN- 68 | 2.89 | 174.42 | H-Bond (Protein Donor) |
| N6A | ND1 | HIS- 89 | 3.48 | 139.58 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 90 | 3.33 | 173.76 | H-Bond (Protein Donor) |
| C3D | CB | ALA- 118 | 3.43 | 0 | Hydrophobic |
| C4D | CG1 | VAL- 167 | 4.32 | 0 | Hydrophobic |
| C5N | CB | SER- 169 | 3.52 | 0 | Hydrophobic |
| O2D | OH | TYR- 182 | 2.88 | 160.54 | H-Bond (Protein Donor) |
| O3D | NZ | LYS- 186 | 3.11 | 144.82 | H-Bond (Protein Donor) |
| O2D | NZ | LYS- 186 | 2.87 | 136.59 | H-Bond (Protein Donor) |
| C5N | CB | PRO- 212 | 3.93 | 0 | Hydrophobic |
| O7N | N | ILE- 215 | 3.04 | 160.1 | H-Bond (Protein Donor) |
| N7N | O | ILE- 215 | 3.5 | 125.76 | H-Bond (Ligand Donor) |
| O1N | OG1 | THR- 217 | 2.58 | 163.13 | H-Bond (Protein Donor) |
| O1A | N | PHE- 219 | 3.48 | 122.49 | H-Bond (Protein Donor) |
| C2D | CE2 | PHE- 219 | 3.89 | 0 | Hydrophobic |
