Fluorine in PDB 5lga: Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D

The structure of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D, PDB code: 5lga was solved by A.Y.Belorusova, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.80 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.860, 65.860, 263.830, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 24.2

The binding sites of Fluorine atom in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D (pdb code 5lga). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D, PDB code: 5lga:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:0.2 occ:1.00 F1 A:6VH501 0.0 0.2 1.0 C26 A:6VH501 1.3 0.5 1.0 F3 A:6VH501 2.1 97.9 1.0 F2 A:6VH501 2.1 0.2 1.0 C24 A:6VH501 2.3 91.7 1.0 F4 A:6VH501 2.5 90.7 1.0 O3 A:6VH501 2.7 89.5 1.0 C25 A:6VH501 2.7 87.7 1.0 F6 A:6VH501 3.1 78.9 1.0 CD1 A:LEU255 3.2 76.4 1.0 C23 A:6VH501 3.6 89.8 1.0 CD2 A:LEU440 3.8 69.7 1.0 F5 A:6VH501 4.0 87.7 1.0 NE2 A:HIS333 4.4 0.8 1.0 CD1 A:LEU430 4.4 97.7 0.0 O A:ALA331 4.6 0.6 1.0 CG A:LEU255 4.7 78.8 1.0 C22 A:6VH501 4.7 89.0 1.0 CB A:ALA259 4.8 63.9 1.0 CA A:ALA259 4.9 63.1 1.0

Fluorine binding site 2 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:0.2 occ:1.00 F2 A:6VH501 0.0 0.2 1.0 C26 A:6VH501 1.3 0.5 1.0 F1 A:6VH501 2.1 0.2 1.0 F3 A:6VH501 2.2 97.9 1.0 C24 A:6VH501 2.4 91.7 1.0 O3 A:6VH501 2.8 89.5 1.0 NE2 A:HIS333 2.9 0.8 1.0 C23 A:6VH501 2.9 89.8 1.0 CD2 A:HIS333 3.5 0.2 1.0 O A:ALA331 3.7 0.6 1.0 C25 A:6VH501 3.7 87.7 1.0 C22 A:6VH501 3.7 89.0 1.0 CE1 A:HIS333 4.0 0.6 1.0 F6 A:6VH501 4.1 78.9 1.0 CD1 A:LEU255 4.1 76.4 1.0 CB A:ALA331 4.1 0.6 1.0 F4 A:6VH501 4.2 90.7 1.0 C A:ALA331 4.7 0.6 1.0 F5 A:6VH501 4.7 87.7 1.0 CB A:LEU258 4.8 69.5 1.0 CD1 A:LEU430 4.8 97.7 0.0 CG A:HIS333 4.8 0.0 1.0 C21 A:6VH501 4.9 90.2 1.0 C27 A:6VH501 4.9 94.7 1.0 C20 A:6VH501 4.9 90.3 1.0

Fluorine binding site 3 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:97.9 occ:1.00 F3 A:6VH501 0.0 97.9 1.0 C26 A:6VH501 1.3 0.5 1.0 F1 A:6VH501 2.1 0.2 1.0 F2 A:6VH501 2.2 0.2 1.0 C24 A:6VH501 2.4 91.7 1.0 F6 A:6VH501 2.5 78.9 1.0 C25 A:6VH501 2.9 87.7 1.0 C23 A:6VH501 2.9 89.8 1.0 F4 A:6VH501 3.5 90.7 1.0 O3 A:6VH501 3.6 89.5 1.0 N A:ALA259 3.7 64.1 1.0 C A:LEU258 3.7 69.5 1.0 C22 A:6VH501 3.7 89.0 1.0 O A:LEU258 3.8 69.8 1.0 CA A:ALA259 3.8 63.1 1.0 CB A:LEU258 4.0 69.5 1.0 F5 A:6VH501 4.1 87.7 1.0 CG2 A:VAL262 4.2 67.2 1.0 CD1 A:LEU255 4.3 76.4 1.0 CB A:ALA259 4.4 63.9 1.0 CA A:LEU258 4.4 67.1 1.0 CB A:VAL262 4.7 65.4 1.0 O A:LEU255 4.8 72.8 1.0 NE2 A:HIS333 4.9 0.8 1.0 C21 A:6VH501 5.0 90.2 1.0

Fluorine binding site 4 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:90.7 occ:1.00 F4 A:6VH501 0.0 90.7 1.0 C25 A:6VH501 1.3 87.7 1.0 F6 A:6VH501 2.2 78.9 1.0 F5 A:6VH501 2.2 87.7 1.0 C24 A:6VH501 2.4 91.7 1.0 F1 A:6VH501 2.5 0.2 1.0 O3 A:6VH501 2.8 89.5 1.0 C26 A:6VH501 3.0 0.5 1.0 CD1 A:TYR427 3.4 72.5 1.0 CE1 A:TYR427 3.5 70.9 1.0 F3 A:6VH501 3.5 97.9 1.0 C23 A:6VH501 3.7 89.8 1.0 CG1 A:VAL444 3.7 66.1 1.0 CD2 A:LEU440 3.7 69.7 1.0 F2 A:6VH501 4.2 0.2 1.0 CD1 A:LEU440 4.4 69.7 1.0 CD2 A:PHE448 4.4 75.4 1.0 CE2 A:PHE448 4.6 77.6 1.0 CG A:LEU440 4.7 68.5 1.0 NE2 A:HIS423 4.7 83.3 1.0 CG A:TYR427 4.7 74.0 1.0 C22 A:6VH501 4.7 89.0 1.0 CZ A:TYR427 4.8 77.2 1.0

Fluorine binding site 5 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:87.7 occ:1.00 F5 A:6VH501 0.0 87.7 1.0 C25 A:6VH501 1.3 87.7 1.0 F4 A:6VH501 2.2 90.7 1.0 F6 A:6VH501 2.2 78.9 1.0 C24 A:6VH501 2.3 91.7 1.0 C23 A:6VH501 2.7 89.8 1.0 O3 A:6VH501 2.8 89.5 1.0 NE2 A:HIS423 3.1 83.3 1.0 CE2 A:PHE448 3.2 77.6 1.0 CE1 A:HIS423 3.5 82.9 1.0 CD2 A:PHE448 3.5 75.4 1.0 C22 A:6VH501 3.5 89.0 1.0 C26 A:6VH501 3.7 0.5 1.0 CD1 A:TYR427 3.8 72.5 1.0 F1 A:6VH501 4.0 0.2 1.0 CZ A:PHE448 4.1 76.9 1.0 F3 A:6VH501 4.1 97.9 1.0 CG1 A:VAL262 4.2 65.2 1.0 CE1 A:TYR427 4.2 70.9 1.0 CG1 A:VAL444 4.3 66.1 1.0 CD2 A:HIS423 4.4 85.8 1.0 CG A:PHE448 4.6 75.8 1.0 CD1 A:ILE296 4.7 84.0 1.0 F2 A:6VH501 4.7 0.2 1.0 C21 A:6VH501 4.7 90.2 1.0 ND1 A:HIS423 4.8 85.4 1.0 CG A:TYR427 4.8 74.0 1.0 CG2 A:VAL262 4.8 67.2 1.0 CB A:VAL262 4.9 65.4 1.0

Fluorine binding site 6 out of 6 in the Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:78.9 occ:1.00 F6 A:6VH501 0.0 78.9 1.0 C25 A:6VH501 1.4 87.7 1.0 F4 A:6VH501 2.2 90.7 1.0 F5 A:6VH501 2.2 87.7 1.0 C24 A:6VH501 2.4 91.7 1.0 F3 A:6VH501 2.5 97.9 1.0 C26 A:6VH501 2.8 0.5 1.0 C23 A:6VH501 2.9 89.8 1.0 F1 A:6VH501 3.1 0.2 1.0 CG1 A:VAL262 3.4 65.2 1.0 CB A:VAL262 3.5 65.4 1.0 CG2 A:VAL262 3.6 67.2 1.0 O3 A:6VH501 3.6 89.5 1.0 C22 A:6VH501 3.7 89.0 1.0 CG1 A:VAL444 3.9 66.1 1.0 F2 A:6VH501 4.1 0.2 1.0 CA A:ALA259 4.2 63.1 1.0 CE2 A:PHE448 4.3 77.6 1.0 O A:LEU258 4.6 69.8 1.0 CG2 A:VAL444 4.6 62.6 1.0 CD2 A:PHE448 4.8 75.4 1.0 CB A:ALA259 4.8 63.9 1.0 CD2 A:LEU440 4.8 69.7 1.0 N A:ALA259 4.9 64.1 1.0 CB A:VAL444 4.9 64.6 1.0 C A:LEU258 5.0 69.5 1.0

A.Y.Belorusova, N.Suh, H.J.Lee, J.Y.So, H.Maehr, N.Rochel. Structural Analysis and Biological Activities of BXL0124, A Gemini Analog of Vitamin D. J. Steroid Biochem. Mol. V. 173 69 2017BIOL..
ISSN: ISSN 1879-1220
PubMed: 27650654
DOI: 10.1016/J.JSBMB.2016.09.015