Chlorine in PDB 8fy1: E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2)

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2), PDB code: 8fy1 was solved by D.Nayak, D.Lv, Y.Yuan, P.Zhang, W.Hu, 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)	80.50 / 2.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.482, 94.593, 81.18, 90, 97.45, 90
R / Rfree (%)	21.2 / 25

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2) also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Chlorine atom in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2) (pdb code 8fy1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2), PDB code: 8fy1:

Chlorine binding site 1 out of 1 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:78.5 occ:1.00 CL01 D:YF8301 0.0 78.5 1.0 C02 D:YF8301 1.7 40.0 1.0 C03 D:YF8301 2.7 53.1 1.0 CAC D:YF8301 2.7 42.1 1.0 CD2 D:PHE112 3.4 65.0 1.0 CG D:GLU152 3.6 68.7 1.0 CE2 D:PHE104 3.7 61.0 1.0 O D:GLU152 3.8 59.3 1.0 C D:GLU152 3.9 62.5 1.0 C04 D:YF8301 4.0 57.5 1.0 CG1 D:VAL156 4.0 56.0 1.0 CE2 D:PHE112 4.0 68.2 1.0 CB D:GLU152 4.0 55.2 1.0 CAB D:YF8301 4.0 54.1 1.0 N D:PHE153 4.1 60.0 1.0 CG D:PHE112 4.3 66.1 1.0 CA D:PHE153 4.3 52.1 1.0 CA D:PHE112 4.4 72.1 1.0 C05 D:YF8301 4.5 56.4 1.0 CB D:PHE112 4.5 70.6 1.0 CD2 D:PHE104 4.5 65.8 1.0 CA D:GLU152 4.6 58.5 1.0 CZ D:PHE104 4.6 65.2 1.0 CB D:PHE153 5.0 57.1 1.0 CG D:MET115 5.0 68.2 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