2.500 Å
X-ray
2012-07-11
Name: | Vitamin D3 receptor A |
---|---|
ID: | VDRA_DANRE |
AC: | Q9PTN2 |
Organism: | Danio rerio |
Reign: | Eukaryota |
TaxID: | 7955 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 63.518 |
---|---|
Number of residues: | 46 |
Including | |
Standard Amino Acids: | 46 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
2.161 | 705.375 |
% Hydrophobic | % Polar |
---|---|
75.60 | 24.40 |
According to VolSite |
HET Code: | 0VP |
---|---|
Formula: | C31H40O4 |
Molecular weight: | 476.647 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 72.43 % |
Polar Surface area: | 69.92 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 4 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 3 |
Anionic atoms: | 0 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 12 |
X | Y | Z |
---|---|---|
1.77891 | 34.0236 | 36.6663 |
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 |
C48 | CZ | TYR- 175 | 4.14 | 0 | Hydrophobic |
C52 | CE2 | TYR- 175 | 4.31 | 0 | Hydrophobic |
O49 | OH | TYR- 175 | 2.72 | 163.79 | H-Bond (Ligand Donor) |
C48 | CE2 | TYR- 179 | 3.65 | 0 | Hydrophobic |
C26 | CD1 | LEU- 255 | 4.12 | 0 | Hydrophobic |
C18 | CD1 | LEU- 258 | 4.42 | 0 | Hydrophobic |
C9 | CB | LEU- 258 | 3.76 | 0 | Hydrophobic |
C29 | CB | ALA- 259 | 4.08 | 0 | Hydrophobic |
C5 | CD2 | LEU- 261 | 3.54 | 0 | Hydrophobic |
C17 | CG2 | VAL- 262 | 4.18 | 0 | Hydrophobic |
C25 | CG1 | VAL- 262 | 4.28 | 0 | Hydrophobic |
C29 | CB | VAL- 262 | 3.81 | 0 | Hydrophobic |
C11 | CG2 | VAL- 262 | 3.78 | 0 | Hydrophobic |
C11 | CG2 | VAL- 262 | 3.78 | 0 | Hydrophobic |
C7 | CG2 | VAL- 262 | 3.97 | 0 | Hydrophobic |
O53 | OG | SER- 265 | 2.83 | 157.57 | H-Bond (Ligand Donor) |
C23 | CD1 | ILE- 296 | 3.37 | 0 | Hydrophobic |
C23 | CG | MET- 300 | 3.4 | 0 | Hydrophobic |
C52 | CG | ARG- 302 | 3.68 | 0 | Hydrophobic |
O53 | NH1 | ARG- 302 | 2.87 | 160.96 | H-Bond (Protein Donor) |
C4 | CB | SER- 303 | 3.98 | 0 | Hydrophobic |
C10 | CB | SER- 303 | 3.84 | 0 | Hydrophobic |
C48 | CB | SER- 306 | 3.65 | 0 | Hydrophobic |
C10 | CE2 | TRP- 314 | 3.96 | 0 | Hydrophobic |
C4 | CB | TRP- 314 | 4.46 | 0 | Hydrophobic |
C4 | SG | CYS- 316 | 3.96 | 0 | Hydrophobic |
C48 | SG | CYS- 316 | 4.1 | 0 | Hydrophobic |
C21 | CG2 | VAL- 328 | 4.19 | 0 | Hydrophobic |
C20 | CG1 | VAL- 328 | 3.71 | 0 | Hydrophobic |
C27 | CG1 | VAL- 328 | 3.49 | 0 | Hydrophobic |
C27 | CB | ALA- 331 | 4.18 | 0 | Hydrophobic |
C9 | CB | ALA- 331 | 4.2 | 0 | Hydrophobic |
O2 | NE2 | HIS- 333 | 2.93 | 168.4 | H-Bond (Ligand Donor) |
C27 | CB | HIS- 333 | 3.94 | 0 | Hydrophobic |
C8 | CD1 | LEU- 338 | 3.7 | 0 | Hydrophobic |
C23 | CD1 | LEU- 341 | 4.42 | 0 | Hydrophobic |
C20 | CD1 | LEU- 341 | 4.03 | 0 | Hydrophobic |
O2 | NE2 | HIS- 423 | 2.61 | 151.05 | H-Bond (Protein Donor) |
C24 | CD1 | TYR- 427 | 4.46 | 0 | Hydrophobic |
C25 | CE1 | TYR- 427 | 4.36 | 0 | Hydrophobic |
C28 | CD1 | TYR- 427 | 3.74 | 0 | Hydrophobic |
C28 | CD2 | LEU- 430 | 3.78 | 0 | Hydrophobic |
C28 | CD2 | LEU- 440 | 3.68 | 0 | Hydrophobic |
C29 | CD2 | LEU- 440 | 4.2 | 0 | Hydrophobic |
C29 | CG1 | VAL- 444 | 4.05 | 0 | Hydrophobic |
C25 | CE1 | PHE- 448 | 4.04 | 0 | Hydrophobic |