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

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

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

Chlorine

(Cl)

2 atoms

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 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 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 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 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 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 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

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