Fluorine in PDB 4fc0: Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor

All present enzymatic activity of Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor:
2.7.11.1;

The structure of Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor, PDB code: 4fc0 was solved by J.K.Yano, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.968, 109.968, 145.973, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.3

The structure of Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor (pdb code 4fc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor, PDB code: 4fc0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:22.3 occ:1.00 F7 A:0T2901 0.0 22.3 1.0 C6 A:0T2901 1.3 21.5 1.0 C5 A:0T2901 2.4 20.2 1.0 C8 A:0T2901 2.4 21.8 1.0 N9 A:0T2901 2.7 23.7 1.0 OE2 A:GLU500 2.8 27.1 1.0 CG2 A:ILE526 3.1 23.4 1.0 CB A:ILE526 3.3 26.4 1.0 CD1 A:LEU504 3.5 23.8 1.0 CG2 A:THR528 3.6 18.4 1.0 C4 A:0T2901 3.6 19.2 1.0 C25 A:0T2901 3.6 19.9 1.0 CE A:LYS482 3.9 30.8 1.0 CD A:GLU500 4.0 28.9 1.0 CD1 A:ILE526 4.0 29.3 1.0 C10 A:0T2901 4.0 26.3 1.0 C3 A:0T2901 4.1 18.6 1.0 CG1 A:ILE526 4.2 29.4 1.0 NZ A:LYS482 4.2 30.7 1.0 O A:ILE526 4.2 25.1 1.0 C A:ILE526 4.4 25.3 1.0 CA A:ILE526 4.5 27.2 1.0 CG A:GLU500 4.6 27.2 1.0 CB A:LYS482 4.7 30.2 1.0 CD A:LYS482 4.7 31.2 1.0 O11 A:0T2901 4.8 25.8 1.0 C12 A:0T2901 4.8 28.9 1.0 CG A:LEU504 4.9 23.4 1.0 OE1 A:GLU500 4.9 31.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Kinase Domain of B-Raf with A Dfg-Out Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:26.4 occ:1.00 F7 B:0T2901 0.0 26.4 1.0 C6 B:0T2901 1.3 25.0 1.0 C8 B:0T2901 2.4 24.7 1.0 C5 B:0T2901 2.4 24.4 1.0 N9 B:0T2901 2.7 26.1 1.0 CG2 B:ILE526 3.0 24.1 1.0 OE2 B:GLU500 3.3 31.0 1.0 CG2 B:THR528 3.4 22.9 1.0 CB B:ILE526 3.5 26.4 1.0 C25 B:0T2901 3.6 23.3 1.0 C4 B:0T2901 3.6 22.8 1.0 CD1 B:LEU504 3.7 24.7 1.0 C10 B:0T2901 3.9 28.8 1.0 C3 B:0T2901 4.1 21.9 1.0 CD1 B:ILE526 4.1 27.7 1.0 CB B:LYS482 4.3 30.2 1.0 O B:ILE526 4.4 26.5 1.0 CD B:GLU500 4.4 31.6 1.0 CG1 B:ILE526 4.4 28.0 1.0 NZ B:LYS482 4.4 29.5 1.0 CD B:LYS482 4.5 30.7 1.0 C B:ILE526 4.6 26.4 1.0 O11 B:0T2901 4.7 29.0 1.0 CA B:ILE526 4.7 27.2 1.0 C12 B:0T2901 4.7 30.7 1.0 CB B:THR528 4.8 22.6 1.0 CG B:GLU500 4.9 29.2 1.0 CG B:LYS482 4.9 31.6 1.0 OG1 B:THR528 5.0 23.9 1.0

M.Hirose, M.Okaniwa, T.Miyazaki, T.Imada, T.Ohashi, Y.Tanaka, T.Arita, M.Yabuki, T.Kawamoto, S.Tsutsumi, A.Sumita, T.Takagi, B.C.Sang, J.Yano, K.Aertgeerts, S.Yoshida, T.Ishikawa. Design and Synthesis of Novel Dfg-Out Raf/Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Inhibitors: 3. Evaluation of 5-Amino-Linked Thiazolo[5,4-D]Pyrimidine and Thiazolo[5,4-B]Pyridine Derivatives. Bioorg.Med.Chem. V. 20 5600 2012.
ISSN: ISSN 0968-0896
PubMed: 22883026
DOI: 10.1016/J.BMC.2012.07.032