Fluorine in PDB 4dbn: Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative

All present enzymatic activity of Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative:
2.7.11.1;

The structure of Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative, PDB code: 4dbn 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 / 3.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.040, 111.040, 146.844, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.3

The structure of Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative (pdb code 4dbn). 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 the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative, PDB code: 4dbn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative


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 the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:42.8 occ:1.00 F1 A:0JA901 0.0 42.8 1.0 C2 A:0JA901 1.4 40.4 1.0 C23 A:0JA901 2.4 38.5 1.0 C3 A:0JA901 2.4 40.4 1.0 N24 A:0JA901 2.7 39.7 1.0 CG2 A:ILE526 3.0 36.7 1.0 OE2 A:GLU500 3.2 41.6 1.0 CD1 A:LEU504 3.5 34.3 1.0 CB A:ILE526 3.5 39.8 1.0 CG2 A:THR528 3.5 31.3 1.0 C22 A:0JA901 3.6 36.8 1.0 C4 A:0JA901 3.6 38.9 1.0 CE A:LYS482 4.0 43.2 1.0 C25 A:0JA901 4.0 40.3 1.0 C5 A:0JA901 4.1 37.5 1.0 CD1 A:ILE526 4.2 43.6 1.0 O A:ILE526 4.3 38.0 1.0 CD A:GLU500 4.3 43.9 1.0 CG1 A:ILE526 4.4 43.0 1.0 C A:ILE526 4.5 37.9 1.0 CB A:LYS482 4.6 43.4 1.0 CA A:ILE526 4.7 40.1 1.0 CG A:GLU500 4.7 43.0 1.0 O26 A:0JA901 4.8 39.0 1.0 C27 A:0JA901 4.8 42.6 1.0 CG A:LEU504 4.8 34.4 1.0 NZ A:LYS482 4.9 45.6 1.0 CB A:THR528 4.9 30.4 1.0 CD A:LYS482 5.0 45.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative


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 the Kinase Domain of Human B-Raf with A [1, 3]Thiazolo[5,4-B]Pyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:44.1 occ:1.00 F1 B:0JA901 0.0 44.1 1.0 C2 B:0JA901 1.3 42.8 1.0 C23 B:0JA901 2.3 41.4 1.0 C3 B:0JA901 2.4 44.5 1.0 N24 B:0JA901 2.6 41.5 1.0 CG2 B:ILE526 2.9 33.7 1.0 CB B:ILE526 3.2 35.9 1.0 CG2 B:THR528 3.4 31.5 1.0 OE2 B:GLU500 3.5 42.3 1.0 C22 B:0JA901 3.6 40.7 1.0 C4 B:0JA901 3.6 44.6 1.0 CD1 B:LEU504 3.9 30.4 1.0 C25 B:0JA901 3.9 41.8 1.0 CG1 B:ILE526 3.9 37.3 1.0 C5 B:0JA901 4.1 42.5 1.0 CE B:LYS482 4.2 41.8 1.0 O B:ILE526 4.3 36.5 1.0 CB B:LYS482 4.3 40.7 1.0 C B:ILE526 4.5 36.0 1.0 CA B:ILE526 4.5 36.9 1.0 CD B:LYS482 4.6 42.4 1.0 CD B:GLU500 4.6 42.3 1.0 NZ B:LYS482 4.6 42.1 1.0 O26 B:0JA901 4.7 39.7 1.0 CB B:THR528 4.7 31.4 1.0 OG1 B:THR528 4.8 32.7 1.0 C27 B:0JA901 4.8 43.1 1.0

M.Okaniwa, M.Hirose, T.Imada, T.Ohashi, Y.Hayashi, T.Miyazaki, T.Arita, M.Yabuki, K.Kakoi, J.Kato, T.Takagi, T.Kawamoto, S.Yao, A.Sumita, S.Tsutsumi, T.Tottori, H.Oki, 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. 1. Exploration of [5,6]-Fused Bicyclic Scaffolds. J.Med.Chem. V. 55 3452 2012.
ISSN: ISSN 0022-2623
PubMed: 22376051
DOI: 10.1021/JM300126X