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Fluorine in PDB 4xv2: B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib

Enzymatic activity of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib

All present enzymatic activity of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib:
2.7.11.1;

Protein crystallography data

The structure of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib, PDB code: 4xv2 was solved by Y.Zhang, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.87 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.689, 105.666, 109.731, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib (pdb code 4xv2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib, PDB code: 4xv2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 1 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:37.5
occ:1.00
 F39 A:P06801 0.0 37.5 1.0
C32 A:P06801 1.3 33.9 1.0
C31 A:P06801 2.3 32.5 1.0
C30 A:P06801 2.4 33.5 1.0
N40 A:P06801 2.7 28.4 1.0
C16 A:P06801 2.8 33.3 1.0
N15 A:P06801 2.9 34.3 1.0
O A:HOH913 3.0 31.0 1.0
N A:ASP594 3.1 38.3 1.0
CA A:ASP594 3.4 38.5 1.0
CB A:ASP594 3.4 41.0 1.0
C33 A:P06801 3.6 29.5 1.0
C35 A:P06801 3.6 31.7 1.0
CE2 A:PHE583 3.9 43.4 1.0
C12 A:P06801 3.9 35.1 1.0
C A:GLY593 3.9 37.8 1.0
CZ A:PHE583 3.9 39.2 1.0
OD1 A:ASP594 4.0 50.0 1.0
C14 A:P06801 4.0 37.0 1.0
CG A:ASP594 4.0 49.2 1.0
C37 A:P06801 4.1 27.3 1.0
CA A:GLY593 4.2 38.5 1.0
S42 A:P06801 4.3 33.8 1.0
NZ A:LYS483 4.3 42.6 1.0
CD2 A:LEU514 4.4 30.7 1.0
C22 A:P06801 4.6 38.1 1.0
C4 A:P06801 4.8 36.2 1.0
S13 A:P06801 4.8 39.5 1.0
C2 A:P06801 4.8 36.7 1.0
CE A:LYS483 4.8 41.7 1.0
O A:GLY593 4.8 34.3 1.0
C A:ASP594 4.9 41.4 1.0
O54 A:P06801 4.9 36.3 1.0
O55 A:P06801 4.9 34.5 1.0
C17 A:P06801 5.0 38.8 1.0
OD2 A:ASP594 5.0 52.6 1.0

Fluorine binding site 2 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 2 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:43.3
occ:1.00
 F52 A:P06801 0.0 43.3 1.0
C49 A:P06801 1.3 39.4 1.0
C50 A:P06801 2.4 38.8 1.0
C43 A:P06801 2.4 38.5 1.0
O55 A:P06801 2.7 34.5 1.0
S42 A:P06801 2.9 33.8 1.0
N40 A:P06801 3.1 28.4 1.0
CA A:GLY593 3.1 38.5 1.0
N A:ASP594 3.3 38.3 1.0
C A:GLY593 3.5 37.8 1.0
C47 A:P06801 3.6 38.8 1.0
C46 A:P06801 3.6 37.2 1.0
CE1 A:PHE595 3.6 52.2 1.0
CD1 A:PHE595 3.7 53.2 1.0
CZ A:PHE595 3.9 53.0 1.0
O A:ILE592 4.0 42.4 1.0
CG A:PHE595 4.0 52.9 1.0
C44 A:P06801 4.1 37.8 1.0
N A:PHE595 4.2 42.4 1.0
C31 A:P06801 4.2 32.5 1.0
CE2 A:PHE595 4.3 55.0 1.0
CD2 A:LEU514 4.3 30.7 1.0
CD2 A:PHE595 4.3 55.4 1.0
CB A:LEU514 4.3 31.1 1.0
N A:GLY593 4.3 39.3 1.0
O54 A:P06801 4.3 36.3 1.0
CA A:ASP594 4.4 38.5 1.0
O A:GLY593 4.5 34.3 1.0
C A:ILE592 4.6 38.8 1.0
CD2 A:LEU505 4.7 38.3 1.0
F53 A:P06801 4.8 34.7 1.0
C A:ASP594 4.8 41.4 1.0
CB A:PHE595 4.8 48.9 1.0
CG A:LEU514 4.9 31.1 1.0
C33 A:P06801 4.9 29.5 1.0

Fluorine binding site 3 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 3 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:34.7
occ:1.00
 F53 A:P06801 0.0 34.7 1.0
C46 A:P06801 1.3 37.2 1.0
C44 A:P06801 2.3 37.8 1.0
C43 A:P06801 2.4 38.5 1.0
O54 A:P06801 2.7 36.3 1.0
S42 A:P06801 3.1 33.8 1.0
CG2 A:ILE527 3.1 38.9 1.0
CD1 A:LEU505 3.3 44.1 1.0
C33 A:P06801 3.5 29.5 1.0
C47 A:P06801 3.6 38.8 1.0
C49 A:P06801 3.6 39.4 1.0
CG2 A:THR529 3.6 28.1 1.0
CB A:ILE527 4.1 37.6 1.0
C50 A:P06801 4.1 38.8 1.0
N40 A:P06801 4.2 28.4 1.0
CD1 A:ILE527 4.2 39.9 1.0
O55 A:P06801 4.2 34.5 1.0
C31 A:P06801 4.3 32.5 1.0
CG A:LEU505 4.4 42.5 1.0
CD2 A:LEU505 4.4 38.3 1.0
C37 A:P06801 4.5 27.3 1.0
CG1 A:ILE527 4.7 39.6 1.0
F52 A:P06801 4.8 43.3 1.0
CB A:LEU505 5.0 41.3 1.0

Fluorine binding site 4 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 4 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:44.6
occ:1.00
 F39 B:P06801 0.0 44.6 1.0
C32 B:P06801 1.3 43.4 1.0
C31 B:P06801 2.3 42.6 1.0
C30 B:P06801 2.4 42.7 1.0
N40 B:P06801 2.7 40.8 1.0
C16 B:P06801 2.8 44.1 1.0
O B:HOH913 2.8 49.0 1.0
N15 B:P06801 2.9 46.9 1.0
N B:ASP594 3.1 43.8 1.0
CB B:ASP594 3.4 46.0 1.0
CA B:ASP594 3.4 45.1 1.0
C33 B:P06801 3.6 42.2 1.0
C35 B:P06801 3.6 42.7 1.0
CZ B:PHE583 3.8 51.9 1.0
C12 B:P06801 3.8 44.5 1.0
C14 B:P06801 3.9 48.2 1.0
C B:GLY593 4.0 38.9 1.0
CE2 B:PHE583 4.0 51.1 1.0
C37 B:P06801 4.1 41.8 1.0
CG B:ASP594 4.1 50.3 1.0
NZ B:LYS483 4.1 49.4 1.0
CA B:GLY593 4.3 32.4 1.0
OD1 B:ASP594 4.3 51.5 1.0
S42 B:P06801 4.3 46.3 1.0
CD2 B:LEU514 4.4 34.0 1.0
C26 B:P06801 4.7 44.7 1.0
C2 B:P06801 4.7 45.8 1.0
CE B:LYS483 4.7 50.7 1.0
S13 B:P06801 4.7 48.1 1.0
C4 B:P06801 4.7 43.9 1.0
O55 B:P06801 4.9 47.1 1.0
O54 B:P06801 4.9 44.8 1.0
C17 B:P06801 4.9 47.9 1.0
O B:GLY593 4.9 38.6 1.0
C B:ASP594 4.9 47.8 1.0
OD2 B:ASP594 5.0 53.5 1.0
CE1 B:PHE583 5.0 51.9 1.0

Fluorine binding site 5 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 5 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:50.0
occ:1.00
 F52 B:P06801 0.0 50.0 1.0
C49 B:P06801 1.3 48.3 1.0
C50 B:P06801 2.4 48.3 1.0
C43 B:P06801 2.4 47.5 1.0
O55 B:P06801 2.8 47.1 1.0
S42 B:P06801 3.0 46.3 1.0
CA B:GLY593 3.1 32.4 1.0
N40 B:P06801 3.2 40.8 1.0
N B:ASP594 3.4 43.8 1.0
CE1 B:PHE595 3.5 66.3 1.0
C B:GLY593 3.6 38.9 1.0
C47 B:P06801 3.6 47.7 1.0
C46 B:P06801 3.6 47.2 1.0
CD1 B:PHE595 3.7 66.5 1.0
CZ B:PHE595 3.8 65.9 1.0
O B:ILE592 3.9 32.6 1.0
CD2 B:LEU514 4.0 34.0 1.0
CG B:PHE595 4.1 64.7 1.0
C44 B:P06801 4.1 47.4 1.0
CB B:LEU514 4.2 35.3 1.0
CE2 B:PHE595 4.2 67.3 1.0
N B:GLY593 4.3 33.0 1.0
CD2 B:PHE595 4.3 67.0 1.0
C31 B:P06801 4.3 42.6 1.0
N B:PHE595 4.4 49.6 1.0
O54 B:P06801 4.4 44.8 1.0
CD2 B:LEU505 4.5 47.9 1.0
C B:ILE592 4.5 33.4 1.0
O B:GLY593 4.5 38.6 1.0
CA B:ASP594 4.5 45.1 1.0
CG B:LEU514 4.7 37.1 1.0
F53 B:P06801 4.8 48.5 1.0
C B:ASP594 4.9 47.8 1.0
C33 B:P06801 5.0 42.2 1.0
CB B:PHE595 5.0 60.5 1.0
O B:LEU514 5.0 38.1 1.0

Fluorine binding site 6 out of 6 in 4xv2

Go back to Fluorine Binding Sites List in 4xv2
Fluorine binding site 6 out of 6 in the B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of B-Raf Kinase V600E Oncogenic Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:48.5
occ:1.00
 F53 B:P06801 0.0 48.5 1.0
C46 B:P06801 1.3 47.2 1.0
C44 B:P06801 2.3 47.4 1.0
C43 B:P06801 2.4 47.5 1.0
O54 B:P06801 2.6 44.8 1.0
S42 B:P06801 3.0 46.3 1.0
CG2 B:ILE527 3.2 42.2 1.0
CD1 B:LEU505 3.3 51.1 1.0
C33 B:P06801 3.5 42.2 1.0
CG2 B:THR529 3.6 43.1 1.0
C47 B:P06801 3.6 47.7 1.0
C49 B:P06801 3.6 48.3 1.0
CB B:ILE527 4.0 47.1 1.0
N40 B:P06801 4.1 40.8 1.0
C50 B:P06801 4.1 48.3 1.0
O55 B:P06801 4.2 47.1 1.0
C31 B:P06801 4.2 42.6 1.0
CD1 B:ILE527 4.2 46.1 1.0
CD2 B:LEU505 4.3 47.9 1.0
CG B:LEU505 4.4 50.8 1.0
C37 B:P06801 4.5 41.8 1.0
CG1 B:ILE527 4.7 47.4 1.0
F52 B:P06801 4.8 50.0 1.0

Reference:

C.Zhang, W.Spevak, Y.Zhang, E.A.Burton, Y.Ma, G.Habets, J.Zhang, J.Lin, T.Ewing, B.Matusow, G.Tsang, A.Marimuthu, H.Cho, G.Wu, W.Wang, D.Fong, H.Nguyen, S.Shi, P.Womack, M.Nespi, R.Shellooe, H.Carias, B.Powell, E.Light, L.Sanftner, J.Walters, J.Tsai, B.L.West, G.Visor, H.Rezaei, P.S.Lin, K.Nolop, P.N.Ibrahim, P.Hirth, G.Bollag. Raf Inhibitors That Evade Paradoxical Mapk Pathway Activation. Nature V. 526 583 2015.
ISSN: ESSN 1476-4687
PubMed: 26466569
DOI: 10.1038/NATURE14982
Page generated: Thu Aug 1 06:48:33 2024

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