Fluorine in PDB 8fy0: E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl)

Protein crystallography data

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl), PDB code: 8fy0 was solved by S.K.Olsen, D.Nayak, D.Lv, Y.Yuan, P.Zhang, W.Hu, Z.Lv, P.Sung, R.Hromas, G.Zheng, D.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.17 / 2.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.62, 118.877, 170.109, 90, 90, 90
R / Rfree (%) 19.5 / 24.1

Other elements in 8fy0:

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

Chlorine (Cl) 1 atom
Arsenic (As) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl) (pdb code 8fy0). 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/753B/Bcl-Xl), PDB code: 8fy0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8fy0

Go back to Fluorine Binding Sites List in 8fy0
Fluorine binding site 1 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl)


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/753B/Bcl-Xl) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:64.0
occ:1.00
 F26 D:YF8301 0.0 64.0 1.0
C25 D:YF8301 1.4 63.1 1.0
F28 D:YF8301 2.2 60.9 1.0
F27 D:YF8301 2.2 66.3 1.0
S23 D:YF8301 2.6 54.1 1.0
O24 D:YF8301 3.0 45.8 1.0
C22 D:YF8301 3.1 48.6 1.0
C21 D:YF8301 3.3 46.1 1.0
CB D:TRP137 3.6 56.2 1.0
O29 D:YF8301 3.8 54.0 1.0
CB D:LEU194 3.8 63.0 1.0
C30 D:YF8301 4.1 47.4 1.0
CG D:TRP137 4.2 62.7 1.0
CD1 D:LEU194 4.2 68.5 1.0
CD1 D:TRP137 4.3 57.5 1.0
C20 D:YF8301 4.4 45.9 1.0
N31 D:YF8301 4.6 45.6 1.0
CG D:LEU194 4.6 65.0 1.0
CD1 D:PHE191 4.6 56.3 1.0
C D:LEU194 4.7 63.8 1.0
CE1 D:PHE191 4.8 61.8 1.0
O D:LEU194 4.8 69.1 1.0
O51 D:YF8301 4.8 50.5 1.0
CA D:TRP137 4.9 53.6 1.0
N D:TYR195 4.9 63.7 1.0
CA D:LEU194 4.9 56.5 1.0
N D:GLY138 4.9 56.4 1.0

Fluorine binding site 2 out of 3 in 8fy0

Go back to Fluorine Binding Sites List in 8fy0
Fluorine binding site 2 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl)


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/753B/Bcl-Xl) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:66.3
occ:1.00
 F27 D:YF8301 0.0 66.3 1.0
C25 D:YF8301 1.4 63.1 1.0
F26 D:YF8301 2.2 64.0 1.0
F28 D:YF8301 2.2 60.9 1.0
S23 D:YF8301 2.6 54.1 1.0
O24 D:YF8301 3.0 45.8 1.0
O29 D:YF8301 3.1 54.0 1.0
CE1 D:PHE191 3.1 61.8 1.0
CD1 D:PHE191 3.1 56.3 1.0
O D:PHE191 3.5 61.5 1.0
N D:TYR195 3.8 63.7 1.0
CB D:TYR195 3.8 58.4 1.0
CA D:TYR195 4.0 62.6 1.0
CB D:LEU194 4.0 63.0 1.0
CZ D:PHE191 4.1 53.7 1.0
C22 D:YF8301 4.1 48.6 1.0
CG D:PHE191 4.1 59.6 1.0
C D:LEU194 4.2 63.8 1.0
CD1 D:TYR195 4.3 59.3 1.0
CB D:TRP137 4.3 56.2 1.0
C D:PHE191 4.4 62.9 1.0
CG D:TYR195 4.6 56.6 1.0
CA D:PHE191 4.6 59.9 1.0
O D:LEU194 4.7 69.1 1.0
CA D:LEU194 4.7 56.5 1.0
CG D:TRP137 4.8 62.7 1.0
C21 D:YF8301 4.8 46.1 1.0
CB D:PHE191 4.9 62.2 1.0
CE2 D:PHE191 4.9 54.9 1.0
CD2 D:PHE191 4.9 52.9 1.0
N31 D:YF8301 4.9 45.6 1.0
C30 D:YF8301 4.9 47.4 1.0

Fluorine binding site 3 out of 3 in 8fy0

Go back to Fluorine Binding Sites List in 8fy0
Fluorine binding site 3 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-Xl)


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/753B/Bcl-Xl) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:60.9
occ:1.00
 F28 D:YF8301 0.0 60.9 1.0
C25 D:YF8301 1.4 63.1 1.0
F26 D:YF8301 2.2 64.0 1.0
F27 D:YF8301 2.2 66.3 1.0
S23 D:YF8301 2.6 54.1 1.0
O29 D:YF8301 2.9 54.0 1.0
C22 D:YF8301 3.3 48.6 1.0
O D:LEU194 3.3 69.1 1.0
N31 D:YF8301 3.4 45.6 1.0
C D:LEU194 3.5 63.8 1.0
N D:TYR195 3.5 63.7 1.0
CA D:TYR195 3.6 62.6 1.0
C30 D:YF8301 3.6 47.4 1.0
O24 D:YF8301 3.8 45.8 1.0
CB D:LEU194 3.9 63.0 1.0
CB D:TYR195 4.1 58.4 1.0
CD1 D:TYR195 4.2 59.3 1.0
C21 D:YF8301 4.2 46.1 1.0
CA D:LEU194 4.3 56.5 1.0
C41 D:YF8301 4.4 48.4 1.0
C32 D:YF8301 4.4 46.7 1.0
CG D:TYR195 4.6 56.6 1.0
C49 D:YF8301 4.7 45.0 1.0
O D:PHE191 4.8 61.5 1.0
C D:TYR195 4.9 69.2 1.0

Reference:

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
Page generated: Fri Aug 2 19:31:15 2024

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