Fluorine in PDB 5hi2: Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib

All present enzymatic activity of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib:
2.7.11.1;

The structure of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib, PDB code: 5hi2 was solved by D.M.Whalen, S.A.Foster, A.Ozen, M.Wongchenko, J.Yin, G.Schaefer, J.Mayfield, J.Chmielecki, P.Stephens, L.Albacker, Y.Yan, K.Song, G.Hatzivassiliou, C.Eigenbrot, C.Yu, A.S.Shaw, G.Manning, N.J.Skelton, S.G.Hymowitz, S.Malek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.56 / 2.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.625, 114.920, 101.544, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.7

The structure of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib (pdb code 5hi2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib, PDB code: 5hi2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:34.0 occ:1.00 F8 A:BAX801 0.0 34.0 1.0 C7 A:BAX801 1.4 27.3 1.0 F9 A:BAX801 2.2 28.1 1.0 F10 A:BAX801 2.3 26.5 1.0 C6 A:BAX801 2.4 19.3 1.0 C1 A:BAX801 2.7 23.2 1.0 O A:ILE592 3.3 21.7 1.0 CA A:GLY593 3.4 22.7 1.0 CG2 A:ILE513 3.4 19.3 1.0 C5 A:BAX801 3.7 18.4 1.0 C A:ILE592 4.0 21.1 1.0 CD2 A:LEU505 4.0 21.2 1.0 C2 A:BAX801 4.1 18.6 1.0 N A:GLY593 4.1 21.5 1.0 C A:GLY593 4.3 23.1 1.0 O15 A:BAX801 4.3 20.3 1.0 CL11 A:BAX801 4.4 37.6 1.0 N A:LEU514 4.4 20.0 1.0 CB A:LEU514 4.6 17.8 1.0 N A:ASP594 4.6 24.6 1.0 O A:LEU514 4.6 18.6 1.0 CB A:ILE513 4.7 19.0 1.0 C4 A:BAX801 4.8 14.6 1.0 N12 A:BAX801 4.9 17.2 1.0 C3 A:BAX801 5.0 16.4 1.0 CA A:LEU514 5.0 17.7 1.0

Fluorine binding site 2 out of 3 in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:28.1 occ:1.00 F9 A:BAX801 0.0 28.1 1.0 C7 A:BAX801 1.4 27.3 1.0 F8 A:BAX801 2.2 34.0 1.0 F10 A:BAX801 2.3 26.5 1.0 C6 A:BAX801 2.4 19.3 1.0 C5 A:BAX801 3.0 18.4 1.0 CL11 A:BAX801 3.0 37.6 1.0 C1 A:BAX801 3.4 23.2 1.0 CD2 A:LEU567 3.7 24.6 1.0 CG2 A:ILE513 3.9 19.3 1.0 CG2 A:THR508 4.0 23.2 1.0 CG1 A:VAL504 4.1 36.9 1.0 CD2 A:LEU505 4.2 21.2 1.0 C4 A:BAX801 4.3 14.6 1.0 CD1 A:LEU567 4.4 22.3 1.0 C2 A:BAX801 4.5 18.6 1.0 OG1 A:THR508 4.7 21.5 1.0 CG A:LEU567 4.7 23.3 1.0 CB A:THR508 4.9 25.1 1.0 C3 A:BAX801 4.9 16.4 1.0

Fluorine binding site 3 out of 3 in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Sorafenib within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:26.5 occ:1.00 F10 A:BAX801 0.0 26.5 1.0 C7 A:BAX801 1.4 27.3 1.0 F8 A:BAX801 2.3 34.0 1.0 F9 A:BAX801 2.3 28.1 1.0 C6 A:BAX801 2.4 19.3 1.0 CL11 A:BAX801 2.9 37.6 1.0 C5 A:BAX801 3.0 18.4 1.0 C1 A:BAX801 3.5 23.2 1.0 CD2 A:HIS574 3.6 21.7 1.0 CD1 A:LEU567 3.6 22.3 1.0 CA A:GLY593 3.8 22.7 1.0 NE2 A:HIS574 3.9 23.1 1.0 CG2 A:ILE592 4.0 19.9 1.0 O A:ILE592 4.1 21.7 1.0 C A:GLY593 4.1 23.1 1.0 C A:ILE592 4.3 21.1 1.0 C4 A:BAX801 4.3 14.6 1.0 N A:GLY593 4.3 21.5 1.0 CD2 A:LEU567 4.4 24.6 1.0 O A:GLY593 4.4 22.2 1.0 CG2 A:ILE513 4.6 19.3 1.0 C2 A:BAX801 4.7 18.6 1.0 CG A:HIS574 4.7 22.4 1.0 CG A:LEU567 4.7 23.3 1.0 N A:ASP594 4.7 24.6 1.0 CB A:ILE592 4.9 19.8 1.0 CD1 A:ILE513 4.9 19.5 1.0 C3 A:BAX801 5.0 16.4 1.0

S.A.Foster, D.M.Whalen, A.Ozen, M.J.Wongchenko, J.Yin, I.Yen, G.Schaefer, J.D.Mayfield, J.Chmielecki, P.J.Stephens, L.A.Albacker, Y.Yan, K.Song, G.Hatzivassiliou, C.Eigenbrot, C.Yu, A.S.Shaw, G.Manning, N.J.Skelton, S.G.Hymowitz, S.Malek. Activation Mechanism of Oncogenic Deletion Mutations in Braf, Egfr, and HER2. Cancer Cell V. 29 477 2016.
ISSN: ISSN 1535-6108
PubMed: 26996308
DOI: 10.1016/J.CCELL.2016.02.010