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Fluorine in PDB 4lvt: BCL_2-Navitoclax (Abt-263) Complex

Protein crystallography data

The structure of BCL_2-Navitoclax (Abt-263) Complex, PDB code: 4lvt was solved by C.H.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.92 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.770, 68.080, 65.470, 90.00, 95.96, 90.00
R / Rfree (%) 16.9 / 22.2

Other elements in 4lvt:

The structure of BCL_2-Navitoclax (Abt-263) Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BCL_2-Navitoclax (Abt-263) Complex (pdb code 4lvt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the BCL_2-Navitoclax (Abt-263) Complex, PDB code: 4lvt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 1 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:23.9
occ:1.00
F59 A:1XJ301 0.0 23.9 1.0
C47 A:1XJ301 1.3 28.9 1.0
F60 A:1XJ301 2.1 24.8 1.0
F61 A:1XJ301 2.2 20.1 1.0
S63 A:1XJ301 2.6 16.5 1.0
CE1 A:PHE195 3.0 18.1 1.0
O55 A:1XJ301 3.0 16.6 1.0
O54 A:1XJ301 3.0 18.6 1.0
CD1 A:PHE195 3.1 16.7 1.0
O A:PHE195 3.7 15.2 1.0
N A:TYR199 3.7 21.0 1.0
CB A:TYR199 3.7 21.7 1.0
CB A:LEU198 3.9 21.1 1.0
C23 A:1XJ301 3.9 17.8 1.0
CA A:TYR199 3.9 22.4 1.0
CZ A:PHE195 4.0 16.9 1.0
CG A:PHE195 4.1 14.9 1.0
C A:LEU198 4.2 24.0 1.0
CB A:TRP141 4.4 10.5 1.0
CG A:LEU198 4.4 28.0 1.0
N51 A:1XJ301 4.5 23.9 1.0
C A:PHE195 4.5 16.0 1.0
CD1 A:TYR199 4.5 22.6 1.0
CA A:PHE195 4.5 14.2 1.0
CD2 A:LEU198 4.6 31.9 1.0
CG A:TYR199 4.6 21.9 1.0
C16 A:1XJ301 4.6 21.6 1.0
C20 A:1XJ301 4.6 34.5 1.0
CA A:LEU198 4.7 19.9 1.0
O A:LEU198 4.7 22.4 1.0
CE2 A:PHE195 4.8 20.8 1.0
CG A:TRP141 4.8 12.1 1.0
CD2 A:PHE195 4.9 18.4 1.0
CB A:PHE195 4.9 15.4 1.0

Fluorine binding site 2 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 2 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:24.8
occ:1.00
F60 A:1XJ301 0.0 24.8 1.0
C47 A:1XJ301 1.4 28.9 1.0
F59 A:1XJ301 2.1 23.9 1.0
F61 A:1XJ301 2.2 20.1 1.0
S63 A:1XJ301 2.6 16.5 1.0
O55 A:1XJ301 3.0 16.6 1.0
C23 A:1XJ301 3.0 17.8 1.0
C16 A:1XJ301 3.2 21.6 1.0
CD2 A:LEU198 3.3 31.9 1.0
CG A:LEU198 3.5 28.0 1.0
CB A:TRP141 3.5 10.5 1.0
CB A:LEU198 3.7 21.1 1.0
O54 A:1XJ301 3.8 18.6 1.0
C20 A:1XJ301 3.9 34.5 1.0
CG A:TRP141 4.1 12.1 1.0
C22 A:1XJ301 4.2 18.6 1.0
O A:HOH420 4.2 45.0 1.0
N51 A:1XJ301 4.3 23.9 1.0
CD1 A:TRP141 4.4 14.8 1.0
CD1 A:PHE195 4.5 16.7 1.0
CE1 A:PHE195 4.6 18.1 1.0
O56 A:1XJ301 4.7 18.4 1.0
C A:LEU198 4.7 24.0 1.0
C10 A:1XJ301 4.8 12.7 1.0
CA A:TRP141 4.8 11.1 1.0
N A:TYR199 4.8 21.0 1.0
CA A:LEU198 4.8 19.9 1.0
C13 A:1XJ301 4.9 24.7 1.0
CD1 A:LEU198 4.9 28.4 1.0
C A:TRP141 4.9 12.3 1.0
O A:LEU198 5.0 22.4 1.0

Fluorine binding site 3 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 3 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:20.1
occ:1.00
F61 A:1XJ301 0.0 20.1 1.0
C47 A:1XJ301 1.4 28.9 1.0
F59 A:1XJ301 2.2 23.9 1.0
F60 A:1XJ301 2.2 24.8 1.0
S63 A:1XJ301 2.6 16.5 1.0
N51 A:1XJ301 2.9 23.9 1.0
O54 A:1XJ301 3.0 18.6 1.0
C23 A:1XJ301 3.1 17.8 1.0
C20 A:1XJ301 3.2 34.5 1.0
O A:LEU198 3.5 22.4 1.0
C A:LEU198 3.5 24.0 1.0
N A:TYR199 3.5 21.0 1.0
CA A:TYR199 3.6 22.4 1.0
O55 A:1XJ301 3.8 16.6 1.0
CB A:LEU198 3.8 21.1 1.0
C46 A:1XJ301 3.9 29.1 1.0
C43 A:1XJ301 3.9 21.9 1.0
CG A:LEU198 4.0 28.0 1.0
C16 A:1XJ301 4.0 21.6 1.0
CB A:TYR199 4.0 21.7 1.0
C10 A:1XJ301 4.3 12.7 1.0
CD1 A:TYR199 4.3 22.6 1.0
CA A:LEU198 4.3 19.9 1.0
O A:HOH420 4.6 45.0 1.0
CD2 A:LEU198 4.6 31.9 1.0
CG A:TYR199 4.7 21.9 1.0
C44 A:1XJ301 4.7 34.6 1.0
C A:TYR199 4.9 31.1 1.0
C22 A:1XJ301 4.9 18.6 1.0
C13 A:1XJ301 5.0 24.7 1.0

Fluorine binding site 4 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 4 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:30.3
occ:1.00
F59 B:1XJ301 0.0 30.3 1.0
C47 B:1XJ301 1.4 42.8 1.0
F61 B:1XJ301 2.1 30.5 1.0
F60 B:1XJ301 2.2 26.5 1.0
S63 B:1XJ301 2.6 26.6 1.0
O55 B:1XJ301 3.0 25.3 1.0
C23 B:1XJ301 3.1 21.1 1.0
C16 B:1XJ301 3.2 22.6 1.0
CD2 B:LEU198 3.6 38.2 1.0
CG B:LEU198 3.6 35.4 1.0
O54 B:1XJ301 3.8 22.9 1.0
CB B:TRP141 3.8 15.1 1.0
C20 B:1XJ301 4.0 30.1 1.0
O B:HOH448 4.0 47.4 1.0
CB B:LEU198 4.0 30.1 1.0
C22 B:1XJ301 4.3 28.2 1.0
N51 B:1XJ301 4.5 31.6 1.0
CG B:TRP141 4.6 15.8 1.0
O56 B:1XJ301 4.8 22.9 1.0
CD1 B:PHE195 4.8 21.6 1.0
CE1 B:PHE195 4.8 23.3 1.0
CD1 B:TRP141 4.8 18.3 1.0
C10 B:1XJ301 4.8 22.6 1.0
C B:LEU198 4.9 33.3 1.0
N B:TYR199 5.0 30.3 1.0
N B:GLY142 5.0 18.6 1.0
C13 B:1XJ301 5.0 38.5 1.0

Fluorine binding site 5 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 5 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:26.5
occ:1.00
F60 B:1XJ301 0.0 26.5 1.0
C47 B:1XJ301 1.4 42.8 1.0
F61 B:1XJ301 2.2 30.5 1.0
F59 B:1XJ301 2.2 30.3 1.0
S63 B:1XJ301 2.6 26.6 1.0
O54 B:1XJ301 2.9 22.9 1.0
C23 B:1XJ301 3.1 21.1 1.0
N51 B:1XJ301 3.2 31.6 1.0
C20 B:1XJ301 3.4 30.1 1.0
O55 B:1XJ301 3.8 25.3 1.0
CA B:TYR199 3.8 31.4 1.0
O B:LEU198 3.9 32.8 1.0
N B:TYR199 4.0 30.3 1.0
C B:LEU198 4.0 33.3 1.0
CD1 B:TYR199 4.0 34.4 1.0
C16 B:1XJ301 4.1 22.6 1.0
CB B:TYR199 4.2 31.7 1.0
C46 B:1XJ301 4.4 38.1 1.0
O B:HOH448 4.4 47.4 1.0
CG B:LEU198 4.4 35.4 1.0
CB B:LEU198 4.4 30.1 1.0
C10 B:1XJ301 4.5 22.6 1.0
CG B:TYR199 4.6 32.7 1.0
C43 B:1XJ301 4.7 42.6 1.0
C44 B:1XJ301 4.7 0.0 1.0
N50 B:1XJ301 4.7 49.2 1.0
CA B:LEU198 4.9 29.4 1.0

Fluorine binding site 6 out of 6 in 4lvt

Go back to Fluorine Binding Sites List in 4lvt
Fluorine binding site 6 out of 6 in the BCL_2-Navitoclax (Abt-263) Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of BCL_2-Navitoclax (Abt-263) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:30.5
occ:1.00
F61 B:1XJ301 0.0 30.5 1.0
C47 B:1XJ301 1.4 42.8 1.0
F59 B:1XJ301 2.1 30.3 1.0
F60 B:1XJ301 2.2 26.5 1.0
S63 B:1XJ301 2.6 26.6 1.0
O55 B:1XJ301 3.0 25.3 1.0
O54 B:1XJ301 3.2 22.9 1.0
CE1 B:PHE195 3.2 23.3 1.0
CD1 B:PHE195 3.4 21.6 1.0
CB B:TYR199 3.7 31.7 1.0
N B:TYR199 3.8 30.3 1.0
CA B:TYR199 3.9 31.4 1.0
C23 B:1XJ301 4.0 21.1 1.0
O B:PHE195 4.0 19.4 1.0
CB B:LEU198 4.1 30.1 1.0
CZ B:PHE195 4.1 23.1 1.0
CD1 B:TYR199 4.2 34.4 1.0
C B:LEU198 4.3 33.3 1.0
CG B:TYR199 4.5 32.7 1.0
CG B:LEU198 4.5 35.4 1.0
CG B:PHE195 4.5 20.6 1.0
CB B:TRP141 4.5 15.1 1.0
C16 B:1XJ301 4.7 22.6 1.0
CD2 B:LEU198 4.7 38.2 1.0
O B:LEU198 4.7 32.8 1.0
N51 B:1XJ301 4.8 31.6 1.0
C20 B:1XJ301 4.8 30.1 1.0
CA B:LEU198 4.8 29.4 1.0
C B:PHE195 4.9 20.1 1.0
CA B:PHE195 5.0 17.1 1.0

Reference:

A.J.Souers, J.D.Leverson, E.R.Boghaert, S.L.Ackler, N.D.Catron, J.Chen, B.D.Dayton, H.Ding, S.H.Enschede, W.J.Fairbrother, D.C.Huang, S.G.Hymowitz, S.Jin, S.L.Khaw, P.J.Kovar, L.T.Lam, J.Lee, H.L.Maecker, K.C.Marsh, K.D.Mason, M.J.Mitten, P.M.Nimmer, A.Oleksijew, C.H.Park, C.M.Park, D.C.Phillips, A.W.Roberts, D.Sampath, J.F.Seymour, M.L.Smith, G.M.Sullivan, S.K.Tahir, C.Tse, M.D.Wendt, Y.Xiao, J.C.Xue, H.Zhang, R.A.Humerickhouse, S.H.Rosenberg, S.W.Elmore. Abt-199, A Potent and Selective Bcl-2 Inhibitor, Achieves Antitumor Activity While Sparing Platelets. Nat.Med. (N.Y.) V. 19 202 2013.
ISSN: ISSN 1078-8956
PubMed: 23291630
DOI: 10.1038/NM.3048
Page generated: Sun Dec 13 12:07:19 2020

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