sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.190 Å
X-ray
2012-11-09
| Name: | Corticosteroid 11-beta-dehydrogenase isozyme 1 |
|---|---|
| ID: | DHI1_HUMAN |
| AC: | P28845 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.146 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 86 % |
| B | 12 % |
| D | 2 % |
| B-Factor: | 31.537 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.623 | 972.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.99 | 42.01 |
| According to VolSite | |
| HET Code: | 19V |
|---|---|
| Formula: | C33H46N7O2 |
| Molecular weight: | 572.764 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.85 % |
| Polar Surface area: | 99.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 8 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 36.3649 | -0.863143 | 12.3325 |
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 | CD1 | ILE- 121 | 3.71 | 0 | Hydrophobic |
| C5 | CB | THR- 124 | 4.31 | 0 | Hydrophobic |
| C8 | CG2 | THR- 124 | 4.15 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 126 | 4.12 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 126 | 3.79 | 0 | Hydrophobic |
| O2 | OG | SER- 170 | 2.7 | 153.88 | H-Bond (Protein Donor) |
| C18 | CB | LEU- 171 | 4.12 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 171 | 3.71 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 171 | 3.65 | 0 | Hydrophobic |
| C21 | CZ | TYR- 177 | 3.47 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 180 | 4.05 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 180 | 4.45 | 0 | Hydrophobic |
| C5 | CE1 | TYR- 183 | 3.64 | 0 | Hydrophobic |
| C6 | CZ | TYR- 183 | 3.6 | 0 | Hydrophobic |
| O2 | OH | TYR- 183 | 2.8 | 127.35 | H-Bond (Protein Donor) |
| N5 | N | LEU- 217 | 2.79 | 142.39 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 217 | 4.38 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 217 | 4.27 | 0 | Hydrophobic |
| C2 | CB | ALA- 223 | 3.83 | 0 | Hydrophobic |
| C9 | CB | ALA- 226 | 3.76 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 227 | 3.75 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 227 | 4.22 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 231 | 4.44 | 0 | Hydrophobic |
| C25 | CE | MET- 233 | 3.86 | 0 | Hydrophobic |
| C23 | CE | MET- 233 | 3.66 | 0 | Hydrophobic |
| C14 | SD | MET- 233 | 4.1 | 0 | Hydrophobic |
| C22 | SD | MET- 233 | 3.95 | 0 | Hydrophobic |
| C31 | CB | SER- 261 | 3.73 | 0 | Hydrophobic |
| C28 | CG2 | THR- 264 | 3.5 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 267 | 4.25 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 276 | 4.03 | 0 | Hydrophobic |
| C32 | CD1 | LEU- 279 | 3.83 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 279 | 3.62 | 0 | Hydrophobic |
| C25 | CD1 | TYR- 280 | 3.64 | 0 | Hydrophobic |
| C22 | CD1 | TYR- 280 | 3.46 | 0 | Hydrophobic |
| C18 | C4N | NDP- 302 | 4.13 | 0 | Hydrophobic |
| C2 | C3N | NDP- 302 | 3.9 | 0 | Hydrophobic |
| N2 | O3 | NDP- 302 | 3.31 | 123.02 | H-Bond (Ligand Donor) |
| N2 | O2N | NDP- 302 | 2.99 | 127.85 | H-Bond (Ligand Donor) |
| N2 | O2A | NDP- 302 | 3.3 | 169.92 | H-Bond (Ligand Donor) |
