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

Protein crystallography data

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

Other elements in 8fy1:

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

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/Bcl-2), PDB code: 8fy1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8fy1

Go back to Fluorine Binding Sites List in 8fy1
Fluorine binding site 1 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/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/753B/Bcl-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:65.0
occ:1.00
 F26 D:YF8301 0.0 65.0 1.0
C25 D:YF8301 1.4 70.9 1.0
F28 D:YF8301 2.2 55.4 1.0
F27 D:YF8301 2.2 75.4 1.0
S23 D:YF8301 2.6 68.4 1.0
O29 D:YF8301 2.8 68.2 1.0
C22 D:YF8301 3.2 56.6 1.0
CB D:LEU201 3.4 73.4 1.0
C21 D:YF8301 3.6 60.0 1.0
O24 D:YF8301 3.7 52.7 1.0
CB D:TRP144 3.8 53.0 1.0
CD1 D:LEU201 3.9 74.1 1.0
C30 D:YF8301 4.2 61.4 1.0
CG D:LEU201 4.3 76.3 1.0
CE1 D:PHE198 4.3 70.1 1.0
CD1 D:PHE198 4.3 66.8 1.0
CG D:TRP144 4.3 59.7 1.0
C D:LEU201 4.4 78.6 1.0
O D:LEU201 4.4 69.4 1.0
N31 D:YF8301 4.4 67.0 1.0
CD1 D:TRP144 4.5 60.6 1.0
CA D:LEU201 4.5 72.7 1.0
N D:TYR202 4.7 83.8 1.0
C20 D:YF8301 4.7 57.7 1.0
O D:PHE198 4.9 69.2 1.0
CD2 D:LEU201 5.0 75.6 1.0

Fluorine binding site 2 out of 3 in 8fy1

Go back to Fluorine Binding Sites List in 8fy1
Fluorine binding site 2 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/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/753B/Bcl-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:75.4
occ:1.00
 F27 D:YF8301 0.0 75.4 1.0
C25 D:YF8301 1.4 70.9 1.0
F26 D:YF8301 2.2 65.0 1.0
F28 D:YF8301 2.2 55.4 1.0
S23 D:YF8301 2.6 68.4 1.0
O24 D:YF8301 2.9 52.7 1.0
O29 D:YF8301 3.0 68.2 1.0
CE1 D:PHE198 3.3 70.1 1.0
CB D:TYR202 3.3 80.5 1.0
N D:TYR202 3.5 83.8 1.0
CD1 D:PHE198 3.6 66.8 1.0
O D:PHE198 3.7 69.2 1.0
CA D:TYR202 3.7 84.0 1.0
CD1 D:TYR202 3.8 75.8 1.0
C D:LEU201 3.8 78.6 1.0
CZ D:PHE198 3.9 74.8 1.0
CB D:LEU201 3.9 73.4 1.0
CG D:TYR202 4.0 75.3 1.0
C22 D:YF8301 4.1 56.6 1.0
O D:LEU201 4.2 69.4 1.0
N31 D:YF8301 4.4 67.0 1.0
CG D:PHE198 4.4 70.1 1.0
CA D:LEU201 4.5 72.7 1.0
CE2 D:PHE198 4.7 72.1 1.0
C30 D:YF8301 4.7 61.4 1.0
C D:PHE198 4.7 73.8 1.0
CD2 D:PHE198 4.9 69.8 1.0
C21 D:YF8301 5.0 60.0 1.0
CE1 D:TYR202 5.0 73.1 1.0

Fluorine binding site 3 out of 3 in 8fy1

Go back to Fluorine Binding Sites List in 8fy1
Fluorine binding site 3 out of 3 in the E3:Protac:Target Ternary Complex Structure (Vcb/753B/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/753B/Bcl-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:55.4
occ:1.00
 F28 D:YF8301 0.0 55.4 1.0
C25 D:YF8301 1.4 70.9 1.0
F26 D:YF8301 2.2 65.0 1.0
F27 D:YF8301 2.2 75.4 1.0
S23 D:YF8301 2.6 68.4 1.0
N31 D:YF8301 2.9 67.0 1.0
O24 D:YF8301 3.0 52.7 1.0
C22 D:YF8301 3.0 56.6 1.0
C30 D:YF8301 3.2 61.4 1.0
O D:LEU201 3.3 69.4 1.0
C41 D:YF8301 3.6 72.7 1.0
C D:LEU201 3.6 78.6 1.0
O29 D:YF8301 3.7 68.2 1.0
C32 D:YF8301 3.9 68.0 1.0
CD1 D:TYR202 3.9 75.8 1.0
N D:TYR202 3.9 83.8 1.0
CA D:TYR202 4.0 84.0 1.0
C21 D:YF8301 4.1 60.0 1.0
CB D:LEU201 4.1 73.4 1.0
CB D:TYR202 4.2 80.5 1.0
C49 D:YF8301 4.3 55.0 1.0
C44 D:YF8301 4.4 83.6 1.0
CA D:LEU201 4.5 72.7 1.0
CG D:TYR202 4.5 75.3 1.0
CE1 D:TYR202 4.9 73.1 1.0
C42 D:YF8301 5.0 86.4 1.0
C20 D:YF8301 5.0 57.7 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 19:31:35 2024

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