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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4dbn:

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

Fluorine Binding Sites:

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 4dbn

Go back to Fluorine Binding Sites List in 4dbn
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 4dbn

Go back to Fluorine Binding Sites List in 4dbn
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

Reference:

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
Page generated: Sun Dec 13 12:01:14 2020

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