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Fluorine in PDB 4ksq: Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B

Enzymatic activity of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B

All present enzymatic activity of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B, PDB code: 4ksq was solved by J.K.Yano, O.Masanori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.829, 110.829, 144.579, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B (pdb code 4ksq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B, PDB code: 4ksq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4ksq

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Fluorine binding site 1 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


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 B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:48.7
occ:1.00
 F1 A:1SW901 0.0 48.7 1.0
C2 A:1SW901 1.4 47.7 1.0
C25 A:1SW901 2.4 47.9 1.0
C3 A:1SW901 2.4 46.8 1.0
N26 A:1SW901 2.7 51.0 1.0
CG2 A:ILE526 3.0 45.4 1.0
CB A:ILE526 3.4 47.3 1.0
CG2 A:THR528 3.6 40.0 1.0
C24 A:1SW901 3.6 45.9 1.0
C4 A:1SW901 3.7 45.5 1.0
OE2 A:GLU500 3.8 51.2 1.0
C27 A:1SW901 3.8 53.2 1.0
CB A:LYS482 3.9 54.4 1.0
O A:ILE526 4.1 46.6 1.0
C5 A:1SW901 4.1 44.6 1.0
CD A:LYS482 4.2 57.5 1.0
C A:ILE526 4.3 45.5 1.0
CD1 A:LEU504 4.3 50.8 1.0
CD1 A:ILE526 4.4 50.1 1.0
CG1 A:ILE526 4.4 49.8 1.0
O28 A:1SW901 4.5 53.8 1.0
CA A:ILE526 4.5 47.1 1.0
N29 A:1SW901 4.5 54.3 1.0
CE A:LYS482 4.6 58.1 1.0
CG A:LYS482 4.7 57.7 1.0
CD A:GLU500 4.8 53.3 1.0
N A:VAL527 4.9 44.2 1.0
N A:LYS482 4.9 51.3 1.0
CB A:THR528 4.9 39.1 1.0
NZ A:LYS482 5.0 58.5 1.0

Fluorine binding site 2 out of 8 in 4ksq

Go back to Fluorine Binding Sites List in 4ksq
Fluorine binding site 2 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


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 B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:53.5
occ:1.00
 F37 A:1SW901 0.0 53.5 1.0
C36 A:1SW901 1.4 55.8 1.0
F39 A:1SW901 2.3 55.6 1.0
F38 A:1SW901 2.3 56.2 1.0
C34 A:1SW901 2.4 56.3 1.0
C33 A:1SW901 2.7 56.7 1.0
C35 A:1SW901 3.7 55.2 1.0
CD1 A:LEU566 3.9 43.4 1.0
C32 A:1SW901 4.1 56.7 1.0
CD2 A:LEU566 4.1 45.8 1.0
CD2 A:HIS573 4.2 49.4 1.0
NE2 A:HIS573 4.5 49.8 1.0
CG A:LEU566 4.7 44.5 1.0
CG1 A:VAL503 4.8 51.1 1.0
C30 A:1SW901 4.8 55.9 1.0
CG2 A:ILE571 4.8 51.6 1.0
CG A:HIS573 4.9 49.2 1.0
C31 A:1SW901 4.9 57.5 1.0

Fluorine binding site 3 out of 8 in 4ksq

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Fluorine binding site 3 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:56.2
occ:1.00
 F38 A:1SW901 0.0 56.2 1.0
C36 A:1SW901 1.4 55.8 1.0
F39 A:1SW901 2.2 55.6 1.0
F37 A:1SW901 2.3 53.5 1.0
C34 A:1SW901 2.4 56.3 1.0
C35 A:1SW901 3.0 55.2 1.0
CA A:GLY592 3.1 47.5 1.0
O A:GLY592 3.2 49.2 1.0
C A:GLY592 3.2 49.3 1.0
O A:ILE591 3.3 43.9 1.0
C33 A:1SW901 3.4 56.7 1.0
N A:GLY592 3.5 44.5 1.0
NE2 A:HIS573 3.5 49.8 1.0
C A:ILE591 3.6 42.9 1.0
CD2 A:HIS573 3.8 49.4 1.0
CG2 A:ILE591 3.9 41.3 1.0
N A:ASP593 4.0 52.1 1.0
C30 A:1SW901 4.3 55.9 1.0
CB A:ILE591 4.5 41.0 1.0
CE1 A:HIS573 4.5 50.4 1.0
C32 A:1SW901 4.6 56.7 1.0
CA A:ILE591 4.7 41.1 1.0
CB A:ASP593 4.9 58.0 1.0
O28 A:1SW901 4.9 53.8 1.0
C31 A:1SW901 4.9 57.5 1.0
CG A:HIS573 5.0 49.2 1.0
CA A:ASP593 5.0 54.8 1.0

Fluorine binding site 4 out of 8 in 4ksq

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Fluorine binding site 4 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:55.6
occ:1.00
 F39 A:1SW901 0.0 55.6 1.0
C36 A:1SW901 1.4 55.8 1.0
F38 A:1SW901 2.2 56.2 1.0
F37 A:1SW901 2.3 53.5 1.0
C34 A:1SW901 2.4 56.3 1.0
C35 A:1SW901 2.8 55.2 1.0
CD2 A:LEU504 3.5 49.1 1.0
C33 A:1SW901 3.5 56.7 1.0
CG2 A:ILE512 3.7 40.6 1.0
O A:ILE591 3.9 43.9 1.0
C30 A:1SW901 4.2 55.9 1.0
CA A:GLY592 4.4 47.5 1.0
C32 A:1SW901 4.7 56.7 1.0
C A:ILE591 4.8 42.9 1.0
O28 A:1SW901 4.8 53.8 1.0
C A:GLY592 4.9 49.3 1.0
CG A:LEU504 4.9 50.3 1.0
C31 A:1SW901 4.9 57.5 1.0
OG1 A:THR507 5.0 40.3 1.0

Fluorine binding site 5 out of 8 in 4ksq

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Fluorine binding site 5 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:53.0
occ:1.00
 F1 B:1SW901 0.0 53.0 1.0
C2 B:1SW901 1.3 51.5 1.0
C25 B:1SW901 2.3 49.5 1.0
C3 B:1SW901 2.4 52.5 1.0
N26 B:1SW901 2.7 50.8 1.0
CG2 B:ILE526 3.1 46.9 1.0
CB B:ILE526 3.4 49.1 1.0
CG2 B:THR528 3.5 43.9 1.0
C4 B:1SW901 3.6 51.3 1.0
C24 B:1SW901 3.6 48.0 1.0
C27 B:1SW901 3.9 50.9 1.0
CB B:LYS482 3.9 55.5 1.0
O B:ILE526 4.0 49.4 1.0
CD1 B:LEU504 4.0 42.5 1.0
CD1 B:ILE526 4.1 50.9 1.0
C5 B:1SW901 4.1 49.0 1.0
OE2 B:GLU500 4.1 54.7 1.0
CD B:LYS482 4.3 58.6 1.0
CG1 B:ILE526 4.3 50.6 1.0
C B:ILE526 4.4 48.8 1.0
N29 B:1SW901 4.5 52.8 1.0
CA B:ILE526 4.6 49.9 1.0
CG B:LYS482 4.6 58.3 1.0
O28 B:1SW901 4.6 49.0 1.0
CB B:THR528 4.8 43.1 1.0
CD B:GLU500 4.9 55.8 1.0
CD2 B:LEU513 4.9 43.2 1.0
N B:LYS482 4.9 53.7 1.0
OG1 B:THR528 5.0 43.7 1.0
CE B:LYS482 5.0 60.4 1.0

Fluorine binding site 6 out of 8 in 4ksq

Go back to Fluorine Binding Sites List in 4ksq
Fluorine binding site 6 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:50.6
occ:1.00
 F37 B:1SW901 0.0 50.6 1.0
C36 B:1SW901 1.4 51.2 1.0
F39 B:1SW901 2.3 51.9 1.0
F38 B:1SW901 2.3 51.2 1.0
C34 B:1SW901 2.4 52.1 1.0
C33 B:1SW901 2.7 52.3 1.0
CD1 B:LEU566 3.5 42.7 1.0
C35 B:1SW901 3.7 51.9 1.0
CD2 B:HIS573 3.8 41.5 1.0
CD2 B:LEU566 4.0 44.8 1.0
C32 B:1SW901 4.1 54.2 1.0
NE2 B:HIS573 4.3 42.2 1.0
CG B:LEU566 4.4 43.4 1.0
CG B:HIS573 4.6 41.8 1.0
CG2 B:ILE571 4.6 47.0 1.0
C30 B:1SW901 4.8 52.8 1.0
CG1 B:VAL503 4.9 48.2 1.0
CG2 B:ILE591 4.9 41.5 1.0
C31 B:1SW901 5.0 54.5 1.0

Fluorine binding site 7 out of 8 in 4ksq

Go back to Fluorine Binding Sites List in 4ksq
Fluorine binding site 7 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:51.2
occ:1.00
 F38 B:1SW901 0.0 51.2 1.0
C36 B:1SW901 1.4 51.2 1.0
F37 B:1SW901 2.3 50.6 1.0
F39 B:1SW901 2.3 51.9 1.0
C34 B:1SW901 2.4 52.1 1.0
C35 B:1SW901 3.0 51.9 1.0
CA B:GLY592 3.1 46.8 1.0
O B:ILE591 3.3 43.8 1.0
C33 B:1SW901 3.4 52.3 1.0
C B:GLY592 3.5 49.3 1.0
N B:GLY592 3.5 43.6 1.0
C B:ILE591 3.6 43.0 1.0
NE2 B:HIS573 3.6 42.2 1.0
O B:GLY592 3.6 48.8 1.0
CG2 B:ILE591 3.7 41.5 1.0
CD2 B:HIS573 3.8 41.5 1.0
C30 B:1SW901 4.3 52.8 1.0
N B:ASP593 4.3 53.0 1.0
CB B:ILE591 4.5 41.1 1.0
C32 B:1SW901 4.6 54.2 1.0
CA B:ILE591 4.7 41.4 1.0
CE1 B:HIS573 4.8 42.3 1.0
CD1 B:LEU566 4.8 42.7 1.0
O28 B:1SW901 4.8 49.0 1.0
CG2 B:ILE512 4.9 40.4 1.0
C31 B:1SW901 4.9 54.5 1.0
CG B:HIS573 5.0 41.8 1.0

Fluorine binding site 8 out of 8 in 4ksq

Go back to Fluorine Binding Sites List in 4ksq
Fluorine binding site 8 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor 5B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:51.9
occ:1.00
 F39 B:1SW901 0.0 51.9 1.0
C36 B:1SW901 1.4 51.2 1.0
F37 B:1SW901 2.3 50.6 1.0
F38 B:1SW901 2.3 51.2 1.0
C34 B:1SW901 2.4 52.1 1.0
C35 B:1SW901 2.9 51.9 1.0
C33 B:1SW901 3.5 52.3 1.0
CG2 B:ILE512 3.5 40.4 1.0
CD2 B:LEU504 3.7 41.4 1.0
O B:ILE591 4.1 43.8 1.0
C30 B:1SW901 4.3 52.8 1.0
CG2 B:THR507 4.5 44.3 1.0
CD2 B:LEU566 4.6 44.8 1.0
C32 B:1SW901 4.7 54.2 1.0
CD1 B:ILE512 4.7 42.0 1.0
CA B:GLY592 4.7 46.8 1.0
CB B:ILE512 4.9 39.5 1.0
CG B:LEU504 4.9 42.4 1.0
C B:ILE591 4.9 43.0 1.0
C31 B:1SW901 5.0 54.5 1.0
CD1 B:LEU566 5.0 42.7 1.0

Reference:

M.Okaniwa, M.Hirose, T.Arita, M.Yabuki, A.Nakamura, T.Takagi, T.Kawamoto, N.Uchiyama, A.Sumita, S.Tsutsumi, T.Tottori, Y.Inui, B.C.Sang, J.Yano, K.Aertgeerts, S.Yoshida, T.Ishikawa. Discovery of A Selective Kinase Inhibitor (Tak-632) Targeting Pan-Raf Inhibition: Design, Synthesis, and Biological Evaluation of C-7-Substituted 1,3-Benzothiazole Derivatives. J.Med.Chem. V. 56 6478 2013.
ISSN: ISSN 0022-2623
PubMed: 23906342
DOI: 10.1021/JM400778D
Page generated: Thu Aug 1 03:17:52 2024

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