Fluorine in PDB 5fd2: B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor

All present enzymatic activity of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor:
2.7.11.1;

The structure of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor, PDB code: 5fd2 was solved by D.A.Whittington, L.F.Epstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.790, 80.088, 245.253, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 27.8

The binding sites of Fluorine atom in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor (pdb code 5fd2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor, PDB code: 5fd2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:27.6 occ:1.00 F31 A:5XJ801 0.0 27.6 1.0 C2 A:5XJ801 1.3 25.9 1.0 C3 A:5XJ801 2.3 26.4 1.0 C1 A:5XJ801 2.4 26.3 1.0 N7 A:5XJ801 2.6 27.2 1.0 N8 A:5XJ801 2.8 27.0 1.0 N14 A:5XJ801 3.2 29.3 1.0 C9 A:5XJ801 3.2 28.7 1.0 N A:ASP594 3.3 29.4 1.0 CD2 A:LEU514 3.4 23.9 1.0 C4 A:5XJ801 3.6 26.4 1.0 C6 A:5XJ801 3.6 25.0 1.0 CA A:GLY593 3.8 25.4 1.0 S24 A:5XJ801 4.0 25.7 1.0 C A:GLY593 4.0 26.9 1.0 C5 A:5XJ801 4.1 24.4 1.0 CA A:ASP594 4.1 31.1 1.0 CE1 A:PHE583 4.2 36.7 1.0 C13 A:5XJ801 4.2 26.9 1.0 N26 A:5XJ801 4.3 27.7 1.0 C29 A:5XJ801 4.4 29.1 1.0 CB A:ASP594 4.4 33.3 1.0 C10 A:5XJ801 4.4 28.5 1.0 CZ A:PHE583 4.5 38.3 1.0 O27 A:5XJ801 4.6 25.2 1.0 F30 A:5XJ801 4.8 24.0 1.0 CG A:LEU514 4.8 22.4 1.0 N16 A:5XJ801 4.8 27.9 1.0

Fluorine binding site 2 out of 4 in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:24.0 occ:1.00 F30 A:5XJ801 0.0 24.0 1.0 C6 A:5XJ801 1.3 25.0 1.0 C5 A:5XJ801 2.3 24.4 1.0 C1 A:5XJ801 2.4 26.3 1.0 N8 A:5XJ801 2.8 27.0 1.0 CB A:ALA481 3.2 28.4 1.0 OG1 A:THR529 3.5 23.6 1.0 O A:ALA481 3.6 25.2 1.0 C4 A:5XJ801 3.6 26.4 1.0 C A:ALA481 3.6 26.6 1.0 C9 A:5XJ801 3.6 28.7 1.0 C2 A:5XJ801 3.6 25.9 1.0 CG1 A:VAL471 3.8 34.8 1.0 CB A:LYS483 3.8 32.5 1.0 N A:LYS483 3.9 29.1 1.0 CA A:ALA481 4.0 27.8 1.0 N A:VAL482 4.1 28.1 1.0 C3 A:5XJ801 4.1 26.4 1.0 C A:VAL482 4.1 29.3 1.0 CG2 A:THR529 4.1 21.4 1.0 N14 A:5XJ801 4.1 29.3 1.0 O A:ILE527 4.2 21.5 1.0 N16 A:5XJ801 4.3 27.9 1.0 CA A:LYS483 4.3 31.6 1.0 CA A:VAL482 4.4 27.7 1.0 CB A:THR529 4.4 21.7 1.0 C10 A:5XJ801 4.5 28.5 1.0 O A:VAL482 4.6 31.2 1.0 N A:THR529 4.7 20.8 1.0 CG2 A:VAL471 4.7 36.3 1.0 F31 A:5XJ801 4.8 27.6 1.0 C15 A:5XJ801 4.8 29.3 1.0 CB A:VAL471 4.8 37.0 1.0 CG A:LYS483 4.9 34.7 1.0

Fluorine binding site 3 out of 4 in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:90.6 occ:1.00 F31 B:5XJ801 0.0 90.6 1.0 C2 B:5XJ801 1.3 82.1 1.0 C1 B:5XJ801 2.4 81.4 1.0 C3 B:5XJ801 2.4 83.7 1.0 N7 B:5XJ801 2.8 72.3 1.0 N8 B:5XJ801 2.8 74.3 1.0 CD2 B:LEU514 3.2 0.4 1.0 C29 B:5XJ801 3.2 63.8 1.0 C9 B:5XJ801 3.5 67.6 1.0 N14 B:5XJ801 3.6 70.7 1.0 N B:ASP594 3.6 77.6 1.0 C6 B:5XJ801 3.6 83.5 1.0 C4 B:5XJ801 3.6 88.8 1.0 CA B:GLY593 3.8 73.4 1.0 C B:GLY593 3.9 73.6 1.0 S24 B:5XJ801 4.0 74.3 1.0 N26 B:5XJ801 4.1 68.2 1.0 C5 B:5XJ801 4.1 81.4 1.0 CE2 B:PHE583 4.2 90.3 1.0 CA B:ASP594 4.4 78.8 1.0 O27 B:5XJ801 4.6 84.4 1.0 CG B:LEU514 4.6 0.9 1.0 CZ B:PHE583 4.6 91.4 1.0 C10 B:5XJ801 4.7 62.0 1.0 C13 B:5XJ801 4.7 67.3 1.0 CB B:ASP594 4.7 77.0 1.0 F30 B:5XJ801 4.7 85.7 1.0 O B:GLY593 4.9 70.8 1.0 N B:GLY593 4.9 69.7 1.0 CB B:LEU514 5.0 0.2 1.0

Fluorine binding site 4 out of 4 in the B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of B-Raf Wild-Type Kinase Domain in Complex with A Purinylpyridinylamino- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:85.7 occ:1.00 F30 B:5XJ801 0.0 85.7 1.0 C6 B:5XJ801 1.3 83.5 1.0 C1 B:5XJ801 2.4 81.4 1.0 C5 B:5XJ801 2.4 81.4 1.0 N8 B:5XJ801 2.7 74.3 1.0 CB B:ALA481 3.1 0.8 1.0 C9 B:5XJ801 3.2 67.6 1.0 C B:ALA481 3.5 0.7 1.0 N14 B:5XJ801 3.6 70.7 1.0 CG2 B:VAL471 3.6 0.1 1.0 C2 B:5XJ801 3.6 82.1 1.0 C4 B:5XJ801 3.6 88.8 1.0 O B:ALA481 3.7 0.6 1.0 OG1 B:THR529 3.7 0.8 1.0 CG1 B:VAL471 3.8 1.0 1.0 N B:VAL482 3.9 0.9 1.0 CA B:ALA481 3.9 0.8 1.0 C10 B:5XJ801 4.0 62.0 1.0 N16 B:5XJ801 4.1 65.3 1.0 C3 B:5XJ801 4.1 83.7 1.0 N B:LYS483 4.2 0.5 1.0 C B:VAL482 4.3 0.4 1.0 CB B:VAL471 4.3 0.9 1.0 C15 B:5XJ801 4.5 68.1 1.0 CA B:VAL482 4.5 0.7 1.0 C13 B:5XJ801 4.6 67.3 1.0 CA B:LYS483 4.6 0.6 1.0 CB B:LYS483 4.6 1.0 1.0 O B:VAL482 4.7 0.5 1.0 F31 B:5XJ801 4.7 90.6 1.0 C11 B:5XJ801 5.0 62.4 1.0

L.Liu, M.R.Lee, J.L.Kim, D.A.Whittington, H.Bregman, Z.Hua, R.T.Lewis, M.W.Martin, N.Nishimura, M.Potashman, K.Yang, S.Yi, K.R.Vaida, L.F.Epstein, C.Babij, M.Fernando, J.Carnahan, M.H.Norman. Purinylpyridinylamino-Based Dfg-in/ Alpha C-Helix-Out B-Raf Inhibitors: Applying Mutant Versus Wild-Type B-Raf Selectivity Indices For Compound Profiling. Bioorg.Med.Chem. V. 24 2215 2016.
ISSN: ESSN 1464-3391
PubMed: 27085672
DOI: 10.1016/J.BMC.2016.03.055