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

Protein crystallography data

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

Other elements in 8fy2:

The structure of E3:Protac:Target Ternary Complex Structure (Vcb/WH244/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/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 8fy2

Go back to Fluorine Binding Sites List in 8fy2
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 8fy2

Go back to Fluorine Binding Sites List in 8fy2
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 8fy2

Go back to Fluorine Binding Sites List in 8fy2
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

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 19:32:08 2024

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy