Fluorine in PDB 8fy2: E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2)

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2), PDB code: 8fy2 was solved by D.Nayak, D.Lv, Y.Yuan, P.Zhang, W.Hu, E.Ruben, Z.Lv, P.Sung, R.Hromas, G.Zheng, D.Zhou, S.K.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.68 / 2.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.278, 102.604, 167.362, 90, 90, 90
R / Rfree (%)	22.9 / 27.9

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2) (pdb code 8fy2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2), PDB code: 8fy2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2) within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:90.6 occ:1.00 F09 D:YFH301 0.0 90.6 1.0 C08 D:YFH301 1.3 79.3 1.0 F10 D:YFH301 2.1 91.2 1.0 F11 D:YFH301 2.1 92.8 1.0 S06 D:YFH301 2.6 87.8 1.0 O07 D:YFH301 2.8 99.7 1.0 CB D:LEU201 3.4 98.2 1.0 O12 D:YFH301 3.4 84.7 1.0 N D:TYR202 3.5 103.1 1.0 C D:LEU201 3.5 111.0 1.0 CB D:TYR202 3.6 101.2 1.0 CA D:TYR202 3.7 104.4 1.0 O D:PHE198 3.8 110.6 1.0 O D:LEU201 3.9 118.5 1.0 CD2 D:TYR202 3.9 97.3 1.0 C05 D:YFH301 4.0 89.6 1.0 CA D:LEU201 4.1 107.2 1.0 N16 D:YFH301 4.1 92.2 1.0 CE1 D:PHE198 4.1 89.3 1.0 CG D:TYR202 4.3 105.4 1.0 CD1 D:PHE198 4.3 91.6 1.0 CG D:LEU201 4.5 92.8 1.0 C15 D:YFH301 4.5 95.2 1.0 N D:LEU201 4.8 112.6 1.0 CZ D:PHE198 4.9 91.8 1.0 C D:PHE198 4.9 114.0 1.0

Fluorine binding site 2 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2) within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:91.2 occ:1.00 F10 D:YFH301 0.0 91.2 1.0 C08 D:YFH301 1.4 79.3 1.0 F09 D:YFH301 2.1 90.6 1.0 F11 D:YFH301 2.2 92.8 1.0 S06 D:YFH301 2.7 87.8 1.0 C05 D:YFH301 3.1 89.6 1.0 O07 D:YFH301 3.4 99.7 1.0 CB D:LEU201 3.5 98.2 1.0 N16 D:YFH301 3.5 92.2 1.0 C15 D:YFH301 3.5 95.2 1.0 O12 D:YFH301 3.7 84.7 1.0 C04 D:YFH301 3.9 91.7 1.0 O D:LEU201 4.0 118.5 1.0 CG D:LEU201 4.0 92.8 1.0 CD1 D:LEU201 4.1 100.7 1.0 C D:LEU201 4.1 111.0 1.0 CA D:LEU201 4.4 107.2 1.0 C14 D:YFH301 4.5 92.4 1.0 C17 D:YFH301 4.6 94.3 1.0 N D:TYR202 4.7 103.1 1.0 C18 D:YFH301 4.9 86.0 1.0 C03 D:YFH301 4.9 93.5 1.0

Fluorine binding site 3 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/Bcl-2) within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:92.8 occ:1.00 F11 D:YFH301 0.0 92.8 1.0 C08 D:YFH301 1.3 79.3 1.0 F09 D:YFH301 2.1 90.6 1.0 F10 D:YFH301 2.2 91.2 1.0 S06 D:YFH301 2.7 87.8 1.0 O12 D:YFH301 2.8 84.7 1.0 CB D:TRP144 3.4 85.2 1.0 CB D:LEU201 3.5 98.2 1.0 O07 D:YFH301 3.7 99.7 1.0 C05 D:YFH301 3.8 89.6 1.0 CD1 D:PHE198 3.9 91.6 1.0 CG D:TRP144 4.0 94.5 1.0 CG D:LEU201 4.1 92.8 1.0 CE1 D:PHE198 4.1 89.3 1.0 C04 D:YFH301 4.1 91.7 1.0 CD1 D:TRP144 4.3 96.2 1.0 O D:PHE198 4.5 110.6 1.0 CA D:TRP144 4.7 83.1 1.0 C15 D:YFH301 4.7 95.2 1.0 CD1 D:LEU201 4.8 100.7 1.0 CA D:LEU201 4.8 107.2 1.0 C D:TRP144 4.8 80.0 1.0 C D:LEU201 4.9 111.0 1.0 N16 D:YFH301 4.9 92.2 1.0 CG D:PHE198 5.0 105.9 1.0

D.Nayak, D.Lv, Y.Yuan, P.Zhang, W.Hu, A.Nayak, E.A.Ruben, Z.Lv, P.Sung, R.Hromas, G.Zheng, D.Zhou, S.K.Olsen. Development and Crystal Structures of A Potent Second-Generation Dual Degrader of Bcl-2 and Bcl-Xl. Nat Commun V. 15 2743 2024.
ISSN: ESSN 2041-1723
PubMed: 38548768
DOI: 10.1038/S41467-024-46922-4