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Fluorine in PDB 4ksp: Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632

Enzymatic activity of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632

All present enzymatic activity of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632, PDB code: 4ksp 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) 35.00 / 2.93
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.495, 111.495, 145.487, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632 (pdb code 4ksp). 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 Tak-632, PDB code: 4ksp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4ksp

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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 Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:87.6
occ:1.00
 F35 A:1SU901 0.0 87.6 1.0
C18 A:1SU901 1.3 86.1 1.0
C15 A:1SU901 2.3 86.4 1.0
C8 A:1SU901 2.4 84.6 1.0
N30 A:1SU901 2.6 82.2 1.0
CG2 A:ILE526 3.0 69.1 1.0
CB A:ILE526 3.5 71.9 1.0
C10 A:1SU901 3.6 88.6 1.0
CG2 A:THR528 3.6 59.6 1.0
C7 A:1SU901 3.6 86.0 1.0
C22 A:1SU901 3.7 82.0 1.0
OE2 A:GLU500 3.8 75.2 1.0
O A:ILE526 4.0 70.9 1.0
CB A:LYS482 4.0 78.9 1.0
C16 A:1SU901 4.1 86.8 1.0
C26 A:1SU901 4.2 87.3 1.0
C A:ILE526 4.3 68.5 1.0
CE A:LYS482 4.3 80.6 1.0
CD A:LYS482 4.4 81.2 1.0
CD1 A:LEU504 4.4 76.8 1.0
CD1 A:ILE526 4.5 79.5 1.0
CA A:ILE526 4.5 71.1 1.0
CG1 A:ILE526 4.5 78.0 1.0
NZ A:LYS482 4.6 80.8 1.0
O33 A:1SU901 4.6 88.3 1.0
CD A:GLU500 4.8 77.3 1.0
CG A:LYS482 4.8 81.7 1.0
N A:VAL527 4.9 66.8 1.0
CB A:THR528 5.0 59.6 1.0
N A:LYS482 5.0 75.2 1.0

Fluorine binding site 2 out of 8 in 4ksp

Go back to Fluorine Binding Sites List in 4ksp
Fluorine binding site 2 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:90.3
occ:1.00
 F36 A:1SU901 0.0 90.3 1.0
C27 A:1SU901 1.4 92.4 1.0
F37 A:1SU901 2.2 89.1 1.0
F38 A:1SU901 2.2 89.5 1.0
C13 A:1SU901 2.4 94.5 1.0
C4 A:1SU901 2.8 0.4 1.0
C9 A:1SU901 3.6 94.2 1.0
CD2 A:HIS573 3.6 65.1 1.0
C2 A:1SU901 4.2 96.3 1.0
CG2 A:ILE571 4.2 69.8 1.0
NE2 A:HIS573 4.3 65.1 1.0
CG1 A:VAL503 4.3 70.8 1.0
CD2 A:LEU566 4.3 66.8 1.0
CD1 A:LEU566 4.3 66.7 1.0
C12 A:1SU901 4.7 99.0 1.0
CG A:HIS573 4.7 62.0 1.0
CG A:LEU566 4.9 66.2 1.0
C3 A:1SU901 4.9 1.0 1.0

Fluorine binding site 3 out of 8 in 4ksp

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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 Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:89.1
occ:1.00
 F37 A:1SU901 0.0 89.1 1.0
C27 A:1SU901 1.4 92.4 1.0
F38 A:1SU901 2.1 89.5 1.0
F36 A:1SU901 2.2 90.3 1.0
C13 A:1SU901 2.4 94.5 1.0
CD2 A:HIS573 3.2 65.1 1.0
C9 A:1SU901 3.2 94.2 1.0
C4 A:1SU901 3.3 0.4 1.0
NE2 A:HIS573 3.3 65.1 1.0
O A:GLY592 3.7 72.1 1.0
CG2 A:ILE591 3.9 60.4 1.0
CA A:GLY592 3.9 69.5 1.0
C A:GLY592 4.0 73.2 1.0
O A:ILE591 4.1 64.4 1.0
N A:GLY592 4.1 63.8 1.0
C A:ILE591 4.2 61.5 1.0
C12 A:1SU901 4.5 99.0 1.0
CD1 A:LEU566 4.5 66.7 1.0
C2 A:1SU901 4.5 96.3 1.0
CG A:HIS573 4.6 62.0 1.0
CE1 A:HIS573 4.6 64.0 1.0
CB A:ILE591 4.8 60.5 1.0
N A:ASP593 4.9 79.7 1.0
C3 A:1SU901 5.0 1.0 1.0

Fluorine binding site 4 out of 8 in 4ksp

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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 Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:89.5
occ:1.00
 F38 A:1SU901 0.0 89.5 1.0
C27 A:1SU901 1.4 92.4 1.0
F37 A:1SU901 2.1 89.1 1.0
F36 A:1SU901 2.2 90.3 1.0
C13 A:1SU901 2.4 94.5 1.0
C9 A:1SU901 2.7 94.2 1.0
C4 A:1SU901 3.6 0.4 1.0
CD2 A:LEU504 3.6 76.2 1.0
C12 A:1SU901 4.0 99.0 1.0
CG2 A:ILE512 4.1 61.4 1.0
C2 A:1SU901 4.7 96.3 1.0
O A:ILE591 4.7 64.4 1.0
CG A:LEU504 4.8 74.3 1.0
C3 A:1SU901 4.9 1.0 1.0
CD2 A:LEU566 4.9 66.8 1.0
C26 A:1SU901 4.9 87.3 1.0
CA A:GLY592 4.9 69.5 1.0
CG1 A:VAL503 5.0 70.8 1.0
OG1 A:THR507 5.0 62.4 1.0

Fluorine binding site 5 out of 8 in 4ksp

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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 Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:76.4
occ:1.00
 F35 B:1SU901 0.0 76.4 1.0
C18 B:1SU901 1.4 75.8 1.0
C8 B:1SU901 2.3 71.0 1.0
C15 B:1SU901 2.4 75.7 1.0
N30 B:1SU901 2.7 76.8 1.0
CG2 B:ILE526 3.1 68.2 1.0
CB B:ILE526 3.3 70.7 1.0
OE2 B:GLU500 3.5 93.0 1.0
C10 B:1SU901 3.6 75.7 1.0
C7 B:1SU901 3.6 68.5 1.0
CD1 B:LEU504 3.7 68.4 1.0
CD1 B:ILE526 3.8 75.2 1.0
CG2 B:THR528 4.0 67.2 1.0
C22 B:1SU901 4.0 77.7 1.0
C16 B:1SU901 4.1 68.8 1.0
CD B:LYS482 4.1 93.9 1.0
CG1 B:ILE526 4.1 74.4 1.0
CB B:LYS482 4.2 86.9 1.0
O B:ILE526 4.5 69.1 1.0
CD B:GLU500 4.5 92.8 1.0
CA B:ILE526 4.6 70.8 1.0
C B:ILE526 4.6 68.5 1.0
C26 B:1SU901 4.7 81.1 1.0
O33 B:1SU901 4.8 73.8 1.0
CG B:LYS482 4.8 91.8 1.0
CG B:GLU500 4.8 85.7 1.0
NZ B:LYS482 4.9 0.9 1.0
CE B:LYS482 5.0 0.0 1.0

Fluorine binding site 6 out of 8 in 4ksp

Go back to Fluorine Binding Sites List in 4ksp
Fluorine binding site 6 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:88.6
occ:1.00
 F36 B:1SU901 0.0 88.6 1.0
C27 B:1SU901 1.4 93.2 1.0
F37 B:1SU901 2.2 92.3 1.0
F38 B:1SU901 2.2 95.7 1.0
C13 B:1SU901 2.4 89.7 1.0
C4 B:1SU901 3.0 91.8 1.0
C9 B:1SU901 3.4 87.8 1.0
CD2 B:HIS573 3.7 61.1 1.0
CG2 B:ILE591 3.8 57.7 1.0
O B:ILE591 3.9 63.2 1.0
NE2 B:HIS573 4.0 61.3 1.0
CA B:GLY592 4.0 86.2 1.0
CD1 B:LEU566 4.1 61.0 1.0
C B:ILE591 4.2 58.9 1.0
N B:GLY592 4.2 81.6 1.0
CD2 B:LEU566 4.3 59.9 1.0
C2 B:1SU901 4.3 94.6 1.0
C12 B:1SU901 4.6 87.6 1.0
CG1 B:ILE512 4.6 63.4 1.0
CB B:ILE591 4.6 56.3 1.0
C B:GLY592 4.7 86.0 1.0
CG2 B:ILE512 4.7 64.2 1.0
CG B:LEU566 4.8 59.1 1.0
CG B:HIS573 4.9 60.1 1.0
C3 B:1SU901 4.9 88.3 1.0
O B:GLY592 5.0 82.2 1.0

Fluorine binding site 7 out of 8 in 4ksp

Go back to Fluorine Binding Sites List in 4ksp
Fluorine binding site 7 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:92.3
occ:1.00
 F37 B:1SU901 0.0 92.3 1.0
C27 B:1SU901 1.4 93.2 1.0
F36 B:1SU901 2.2 88.6 1.0
F38 B:1SU901 2.2 95.7 1.0
C13 B:1SU901 2.4 89.7 1.0
C9 B:1SU901 2.7 87.8 1.0
CD2 B:LEU504 3.4 66.4 1.0
C4 B:1SU901 3.6 91.8 1.0
CG2 B:ILE512 3.9 64.2 1.0
C12 B:1SU901 4.0 87.6 1.0
O B:ILE591 4.4 63.2 1.0
CA B:GLY592 4.6 86.2 1.0
CG B:LEU504 4.7 66.6 1.0
C2 B:1SU901 4.7 94.6 1.0
CG2 B:THR507 4.8 64.0 1.0
CG1 B:ILE512 4.8 63.4 1.0
O33 B:1SU901 4.9 73.8 1.0
C3 B:1SU901 4.9 88.3 1.0
C26 B:1SU901 4.9 81.1 1.0
CD2 B:LEU566 4.9 59.9 1.0
OG1 B:THR507 4.9 59.6 1.0

Fluorine binding site 8 out of 8 in 4ksp

Go back to Fluorine Binding Sites List in 4ksp
Fluorine binding site 8 out of 8 in the Crystal Structure of Human B-Raf Bound to A Dfg-Out Inhibitor Tak-632


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 Tak-632 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:95.7
occ:1.00
 F38 B:1SU901 0.0 95.7 1.0
C27 B:1SU901 1.4 93.2 1.0
F37 B:1SU901 2.2 92.3 1.0
F36 B:1SU901 2.2 88.6 1.0
C13 B:1SU901 2.4 89.7 1.0
C4 B:1SU901 3.0 91.8 1.0
C9 B:1SU901 3.4 87.8 1.0
CD2 B:LEU566 3.7 59.9 1.0
CG1 B:VAL503 4.0 67.8 1.0
CG2 B:ILE571 4.2 68.4 1.0
C2 B:1SU901 4.3 94.6 1.0
CD1 B:LEU566 4.3 61.0 1.0
C12 B:1SU901 4.6 87.6 1.0
CG2 B:THR507 4.6 64.0 1.0
CG B:LEU566 4.6 59.1 1.0
CD2 B:HIS573 4.8 61.1 1.0
CD2 B:LEU504 4.9 66.4 1.0
CD1 B:ILE571 4.9 75.2 1.0
C3 B:1SU901 4.9 88.3 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 03:17:50 2024

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