Fluorine in PDB 3c4c: B-Raf Kinase in Complex with PLX4720

All present enzymatic activity of B-Raf Kinase in Complex with PLX4720:
2.7.11.1;

The structure of B-Raf Kinase in Complex with PLX4720, PDB code: 3c4c was solved by K.Y.J.Zhang, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.574, 105.502, 110.150, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 30.3

The structure of B-Raf Kinase in Complex with PLX4720 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the B-Raf Kinase in Complex with PLX4720 (pdb code 3c4c). 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 Kinase in Complex with PLX4720, PDB code: 3c4c:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the B-Raf Kinase in Complex with PLX4720


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of B-Raf Kinase in Complex with PLX4720 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:25.6 occ:1.00 F20 A:3242 0.0 25.6 1.0 C18 A:3242 1.3 24.8 1.0 C13 A:3242 2.3 24.9 1.0 C17 A:3242 2.5 24.4 1.0 C11 A:3242 2.6 26.0 1.0 O12 A:3242 2.8 29.9 1.0 N21 A:3242 2.9 24.7 1.0 CE1 A:PHE583 3.0 25.5 1.0 CZ A:PHE583 3.2 25.9 1.0 O A:HOH798 3.3 25.2 1.0 C9 A:3242 3.5 25.0 1.0 CD2 A:LEU514 3.5 25.9 1.0 N A:ASP594 3.6 27.0 1.0 C14 A:3242 3.7 24.2 1.0 C16 A:3242 3.7 24.9 1.0 C8 A:3242 4.0 24.9 1.0 C15 A:3242 4.2 24.0 1.0 C A:GLY593 4.3 26.8 1.0 CD1 A:PHE583 4.3 26.0 1.0 CA A:GLY593 4.3 26.3 1.0 CA A:ASP594 4.3 27.2 1.0 CE2 A:PHE583 4.5 27.1 1.0 CB A:ASP594 4.5 27.6 1.0 S22 A:3242 4.5 28.2 1.0 C2 A:3242 4.7 24.8 1.0 F19 A:3242 4.7 25.5 1.0 CG A:LEU514 4.9 25.3 1.0

Fluorine binding site 2 out of 4 in the B-Raf Kinase in Complex with PLX4720


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of B-Raf Kinase in Complex with PLX4720 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:25.5 occ:1.00 F19 A:3242 0.0 25.5 1.0 C14 A:3242 1.3 24.2 1.0 C15 A:3242 2.3 24.0 1.0 C13 A:3242 2.4 24.9 1.0 C11 A:3242 3.0 26.0 1.0 C9 A:3242 3.3 25.0 1.0 CB A:ALA481 3.4 24.2 1.0 C8 A:3242 3.6 24.9 1.0 C16 A:3242 3.6 24.9 1.0 CB A:LYS483 3.7 24.2 1.0 C18 A:3242 3.7 24.8 1.0 N A:LYS483 3.7 23.6 1.0 CG1 A:VAL471 3.8 26.1 1.0 O12 A:3242 3.8 29.9 1.0 C A:ALA481 3.8 24.4 1.0 N A:VAL482 3.9 24.0 1.0 CG2 A:VAL471 4.0 24.4 1.0 O A:ALA481 4.1 24.9 1.0 C A:VAL482 4.1 24.0 1.0 CA A:LYS483 4.2 24.0 1.0 C17 A:3242 4.2 24.4 1.0 CA A:ALA481 4.2 24.2 1.0 OG1 A:THR529 4.3 22.2 1.0 CA A:VAL482 4.4 24.2 1.0 C2 A:3242 4.4 24.8 1.0 CB A:VAL471 4.4 24.8 1.0 N7 A:3242 4.6 24.7 1.0 O A:VAL482 4.7 24.2 1.0 F20 A:3242 4.7 25.6 1.0 CG2 A:THR529 4.8 23.5 1.0 O A:ILE527 4.8 23.7 1.0 CG A:LYS483 4.9 25.1 1.0 CD A:LYS483 4.9 26.3 1.0 CA A:VAL471 5.0 24.7 1.0

Fluorine binding site 3 out of 4 in the B-Raf Kinase in Complex with PLX4720


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of B-Raf Kinase in Complex with PLX4720 within 5.0Å range: probe atom residue distance (Å) B Occ B:F3 b:27.3 occ:0.60 F20 B:3243 0.0 27.3 0.6 C18 B:3243 1.4 26.5 0.6 C13 B:3243 2.4 26.3 0.6 C17 B:3243 2.5 25.8 0.6 C11 B:3243 2.9 25.5 0.6 N21 B:3243 2.9 25.5 0.6 O B:ASP594 3.1 26.8 1.0 O12 B:3243 3.1 23.9 0.6 C16 B:3243 3.7 25.6 0.6 C14 B:3243 3.8 26.7 0.6 C9 B:3243 3.8 25.3 0.6 C15 B:3243 4.2 26.2 0.6 C B:ASP594 4.3 26.7 1.0 C B:PHE595 4.3 28.3 1.0 O B:PHE595 4.4 29.4 1.0 CD1 B:LEU514 4.4 25.1 1.0 NZ B:LYS483 4.4 25.9 1.0 C8 B:3243 4.5 25.4 0.6 S22 B:3243 4.5 25.0 0.6 N B:ASP594 4.7 26.0 1.0 CE B:LYS483 4.8 26.7 1.0 C2 B:3243 4.9 26.0 0.6 F19 B:3243 4.9 27.8 0.6 C B:GLY593 5.0 26.1 1.0

Fluorine binding site 4 out of 4 in the B-Raf Kinase in Complex with PLX4720


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of B-Raf Kinase in Complex with PLX4720 within 5.0Å range: probe atom residue distance (Å) B Occ B:F3 b:27.8 occ:0.60 F19 B:3243 0.0 27.8 0.6 C14 B:3243 1.3 26.7 0.6 C15 B:3243 2.4 26.2 0.6 C13 B:3243 2.5 26.3 0.6 C11 B:3243 2.9 25.5 0.6 CG1 B:VAL471 3.1 26.9 1.0 C9 B:3243 3.2 25.3 0.6 C8 B:3243 3.3 25.4 0.6 O B:ALA481 3.5 26.6 1.0 C16 B:3243 3.6 25.6 0.6 O12 B:3243 3.7 23.9 0.6 CB B:ALA481 3.7 25.8 1.0 CB B:LYS483 3.7 26.7 1.0 C18 B:3243 3.8 26.5 0.6 N B:LYS483 3.9 26.7 1.0 OG1 B:THR529 3.9 23.9 1.0 C B:ALA481 3.9 26.2 1.0 CA B:LYS483 4.2 26.9 1.0 C17 B:3243 4.2 25.8 0.6 C B:VAL482 4.2 26.5 1.0 O B:ILE527 4.3 25.6 1.0 CG B:LYS483 4.3 26.6 1.0 C2 B:3243 4.3 26.0 0.6 CB B:VAL471 4.4 26.8 1.0 N7 B:3243 4.4 25.8 0.6 CG2 B:THR529 4.5 25.1 1.0 CA B:ALA481 4.5 25.9 1.0 N B:VAL482 4.5 26.3 1.0 O B:VAL482 4.7 26.5 1.0 CA B:VAL482 4.7 26.3 1.0 CB B:THR529 4.9 24.9 1.0 F20 B:3243 4.9 27.3 0.6 C3 B:3243 4.9 25.9 0.6

J.Tsai, J.T.Lee, W.Wang, J.Zhang, H.Cho, S.Mamo, R.Bremer, S.Gillette, J.Kong, N.K.Haass, K.Sproesser, L.Li, K.S.Smalley, D.Fong, Y.L.Zhu, A.Marimuthu, H.Nguyen, B.Lam, J.Liu, I.Cheung, J.Rice, Y.Suzuki, C.Luu, C.Settachatgul, R.Shellooe, J.Cantwell, S.H.Kim, J.Schlessinger, K.Y.Zhang, B.L.West, B.Powell, G.Habets, C.Zhang, P.N.Ibrahim, P.Hirth, D.R.Artis, M.Herlyn, G.Bollag. Discovery of A Selective Inhibitor of Oncogenic B-Raf Kinase with Potent Antimelanoma Activity Proc.Natl.Acad.Sci.Usa V. 105 3041 2008.
ISSN: ISSN 0027-8424
PubMed: 18287029
DOI: 10.1073/PNAS.0711741105