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Fluorine in PDB 5hie: Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib

Enzymatic activity of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib

All present enzymatic activity of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib:
2.7.11.1;

Protein crystallography data

The structure of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib, PDB code: 5hie was solved by D.M.Whalen, S.A.Foster, A.Ozen, M.Wongchenko, J.Yin, G.Schaefer, J.Mayfield, J.Chmielecki, P.Stephens, L.Albacker, Y.Yan, K.Song, G.Hatzivassiliou, C.Eigenbrot, C.Yu, A.S.Shaw, G.Manning, N.J.Skelton, S.G.Hymowitz, S.Malek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.28 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.413, 127.786, 83.135, 90.00, 105.79, 90.00
R / Rfree (%) 19.4 / 22.1

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib (pdb code 5hie). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib, PDB code: 5hie:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5hie

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Fluorine binding site 1 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:36.9
occ:1.00
 F39 A:P06801 0.0 36.9 1.0
C32 A:P06801 1.4 35.0 1.0
C30 A:P06801 2.4 34.4 1.0
C31 A:P06801 2.4 33.0 1.0
N40 A:P06801 2.7 32.9 1.0
C16 A:P06801 2.8 34.6 1.0
N A:ASP594 2.9 28.3 1.0
N15 A:P06801 3.0 33.2 1.0
CA A:ASP594 3.4 28.4 1.0
CB A:ASP594 3.5 29.8 1.0
CZ A:PHE583 3.6 40.1 1.0
CE2 A:PHE583 3.7 41.7 1.0
C35 A:P06801 3.7 31.4 1.0
C33 A:P06801 3.7 31.1 1.0
C12 A:P06801 3.8 35.1 1.0
C A:GLY593 3.8 31.6 1.0
C14 A:P06801 4.0 32.0 1.0
CA A:GLY593 4.1 29.4 1.0
C37 A:P06801 4.2 30.3 1.0
CD2 A:LEU514 4.2 28.9 1.0
OD1 A:ASP594 4.3 47.1 1.0
CG A:ASP594 4.3 44.0 1.0
S42 A:P06801 4.3 33.8 1.0
NZ A:LYS483 4.6 49.6 1.0
C4 A:P06801 4.6 38.2 1.0
C2 A:P06801 4.6 37.1 1.0
C22 A:P06801 4.7 25.8 1.0
S13 A:P06801 4.7 34.8 1.0
CE A:LYS483 4.7 42.8 1.0
O55 A:P06801 4.8 33.4 1.0
O A:GLY593 4.8 30.0 1.0
O54 A:P06801 4.9 34.5 1.0
C A:ASP594 4.9 33.3 1.0
CE1 A:PHE583 4.9 40.9 1.0
F53 A:P06801 4.9 34.7 1.0
C17 A:P06801 5.0 27.1 1.0
CD2 A:PHE583 5.0 38.5 1.0

Fluorine binding site 2 out of 12 in 5hie

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Fluorine binding site 2 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:38.3
occ:1.00
 F52 A:P06801 0.0 38.3 1.0
C49 A:P06801 1.4 37.9 1.0
C50 A:P06801 2.3 37.7 1.0
C43 A:P06801 2.4 36.5 1.0
O54 A:P06801 2.7 34.5 1.0
S42 A:P06801 3.1 33.8 1.0
CG2 A:ILE527 3.3 43.3 1.0
CD2 A:LEU505 3.4 68.4 1.0
C47 A:P06801 3.6 37.3 1.0
C46 A:P06801 3.7 35.3 1.0
CE2 A:PHE498 3.7 56.6 1.0
CD1 A:ILE527 3.7 53.6 1.0
C33 A:P06801 3.9 31.1 1.0
CG2 A:THR529 4.1 34.6 1.0
C44 A:P06801 4.1 35.7 1.0
CB A:ILE527 4.1 43.8 1.0
O55 A:P06801 4.2 33.4 1.0
N40 A:P06801 4.2 32.9 1.0
CZ A:PHE498 4.2 54.2 1.0
CG1 A:ILE527 4.5 46.1 1.0
C31 A:P06801 4.5 33.0 1.0
CD2 A:PHE498 4.6 55.1 1.0
CG A:LEU505 4.7 67.5 1.0
CZ A:PHE468 4.8 55.2 1.0
F53 A:P06801 4.8 34.7 1.0
CD A:LYS483 4.8 30.5 1.0
C37 A:P06801 4.9 30.3 1.0

Fluorine binding site 3 out of 12 in 5hie

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Fluorine binding site 3 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion 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 35.3 1.0
C44 A:P06801 2.4 35.7 1.0
C43 A:P06801 2.4 36.5 1.0
O55 A:P06801 2.9 33.4 1.0
S42 A:P06801 3.0 33.8 1.0
N40 A:P06801 3.0 32.9 1.0
CA A:GLY593 3.2 29.4 1.0
CD1 A:PHE595 3.3 37.0 1.0
CE1 A:PHE595 3.4 37.2 1.0
C47 A:P06801 3.6 37.3 1.0
C49 A:P06801 3.7 37.9 1.0
N A:ASP594 3.8 28.3 1.0
CB A:LEU514 3.8 24.6 1.0
C A:GLY593 3.9 31.6 1.0
O A:ILE592 4.0 34.3 1.0
CD2 A:LEU514 4.0 28.9 1.0
C31 A:P06801 4.1 33.0 1.0
C50 A:P06801 4.1 37.7 1.0
O54 A:P06801 4.3 34.5 1.0
N A:GLY593 4.4 29.6 1.0
CG A:LEU514 4.5 28.4 1.0
CG A:PHE595 4.5 34.7 1.0
C A:ILE592 4.6 32.9 1.0
O A:LEU514 4.6 31.0 1.0
CZ A:PHE595 4.7 36.6 1.0
N A:PHE595 4.7 32.0 1.0
CG2 A:VAL504 4.7 60.8 1.0
C33 A:P06801 4.8 31.1 1.0
F52 A:P06801 4.8 38.3 1.0
CA A:LEU514 4.8 25.6 1.0
O A:GLY593 4.9 30.0 1.0
CA A:ASP594 4.9 28.4 1.0
F39 A:P06801 4.9 36.9 1.0
N A:LEU514 4.9 25.9 1.0
C32 A:P06801 4.9 35.0 1.0

Fluorine binding site 4 out of 12 in 5hie

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Fluorine binding site 4 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:40.4
occ:1.00
 F39 B:P06801 0.0 40.4 1.0
C32 B:P06801 1.4 37.2 1.0
C30 B:P06801 2.4 34.5 1.0
C31 B:P06801 2.4 35.1 1.0
N40 B:P06801 2.7 34.3 1.0
C16 B:P06801 2.8 33.9 1.0
N B:ASP594 2.8 31.5 1.0
N15 B:P06801 2.9 33.4 1.0
CA B:ASP594 3.2 33.5 1.0
CB B:ASP594 3.3 35.4 1.0
C35 B:P06801 3.6 33.2 1.0
C33 B:P06801 3.7 34.8 1.0
C B:GLY593 3.8 32.5 1.0
CZ B:PHE583 3.9 41.6 1.0
C14 B:P06801 3.9 32.9 1.0
C12 B:P06801 3.9 32.8 1.0
CE2 B:PHE583 3.9 42.8 1.0
OD1 B:ASP594 4.1 50.5 1.0
CG B:ASP594 4.1 47.9 1.0
CA B:GLY593 4.1 26.8 1.0
C37 B:P06801 4.1 34.0 1.0
NZ B:LYS483 4.3 61.8 1.0
C22 B:P06801 4.3 31.3 1.0
S42 B:P06801 4.4 33.6 1.0
CD2 B:LEU514 4.4 34.9 1.0
CE B:LYS483 4.6 54.2 1.0
C B:ASP594 4.7 39.2 1.0
O B:GLY593 4.8 31.6 1.0
O55 B:P06801 4.8 33.0 1.0
C17 B:P06801 4.8 32.0 1.0
S13 B:P06801 4.8 33.1 1.0
C2 B:P06801 4.9 30.6 1.0
F53 B:P06801 4.9 39.7 1.0
O54 B:P06801 4.9 29.5 1.0
C4 B:P06801 5.0 30.3 1.0

Fluorine binding site 5 out of 12 in 5hie

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Fluorine binding site 5 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:34.1
occ:1.00
 F52 B:P06801 0.0 34.1 1.0
C49 B:P06801 1.3 34.0 1.0
C50 B:P06801 2.4 32.5 1.0
C43 B:P06801 2.4 35.3 1.0
O54 B:P06801 2.7 29.5 1.0
S42 B:P06801 3.1 33.6 1.0
CG2 B:ILE527 3.2 36.4 1.0
CD1 B:LEU505 3.4 56.7 1.0
C47 B:P06801 3.6 32.1 1.0
C46 B:P06801 3.7 36.1 1.0
C33 B:P06801 3.7 34.8 1.0
CD1 B:ILE527 3.7 50.6 1.0
CG2 B:THR529 3.9 40.7 1.0
CE2 B:PHE498 3.9 52.4 1.0
CB B:ILE527 4.0 37.5 1.0
C44 B:P06801 4.1 32.6 1.0
N40 B:P06801 4.2 34.3 1.0
O55 B:P06801 4.2 33.0 1.0
C31 B:P06801 4.4 35.1 1.0
CG1 B:ILE527 4.4 39.7 1.0
CZ B:PHE498 4.4 49.8 1.0
C37 B:P06801 4.7 34.0 1.0
CD B:LYS483 4.7 40.5 1.0
F53 B:P06801 4.8 39.7 1.0
CG B:LEU505 4.8 58.7 1.0
CD2 B:PHE498 4.9 51.2 1.0
CZ B:PHE468 5.0 49.0 1.0

Fluorine binding site 6 out of 12 in 5hie

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Fluorine binding site 6 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:39.7
occ:1.00
 F53 B:P06801 0.0 39.7 1.0
C46 B:P06801 1.4 36.1 1.0
C44 B:P06801 2.4 32.6 1.0
C43 B:P06801 2.4 35.3 1.0
O55 B:P06801 2.8 33.0 1.0
S42 B:P06801 2.9 33.6 1.0
N40 B:P06801 3.0 34.3 1.0
CD1 B:PHE595 3.1 40.5 1.0
CE1 B:PHE595 3.2 40.5 1.0
CA B:GLY593 3.3 26.8 1.0
C47 B:P06801 3.6 32.1 1.0
C49 B:P06801 3.6 34.0 1.0
N B:ASP594 3.7 31.5 1.0
C B:GLY593 3.8 32.5 1.0
C31 B:P06801 4.0 35.1 1.0
O B:ILE592 4.1 31.5 1.0
C50 B:P06801 4.1 32.5 1.0
CB B:LEU514 4.1 28.9 1.0
CD2 B:LEU514 4.2 34.9 1.0
O54 B:P06801 4.3 29.5 1.0
CG B:PHE595 4.3 38.8 1.0
CG2 B:VAL504 4.5 56.4 1.0
N B:GLY593 4.5 25.9 1.0
N B:PHE595 4.5 36.1 1.0
CZ B:PHE595 4.5 39.9 1.0
C33 B:P06801 4.7 34.8 1.0
C B:ILE592 4.7 30.2 1.0
CA B:ASP594 4.8 33.5 1.0
CG B:LEU514 4.8 32.5 1.0
F52 B:P06801 4.8 34.1 1.0
O B:GLY593 4.8 31.6 1.0
O B:LEU514 4.9 35.5 1.0
C32 B:P06801 4.9 37.2 1.0
F39 B:P06801 4.9 40.4 1.0
CB B:PHE595 4.9 38.6 1.0

Fluorine binding site 7 out of 12 in 5hie

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Fluorine binding site 7 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 7 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:57.3
occ:1.00
 F39 C:P06801 0.0 57.3 1.0
C32 C:P06801 1.3 53.8 1.0
C31 C:P06801 2.4 51.5 1.0
C30 C:P06801 2.4 52.3 1.0
N40 C:P06801 2.7 51.3 1.0
C16 C:P06801 2.8 54.0 1.0
N15 C:P06801 2.8 54.9 1.0
N C:ASP594 2.9 63.8 1.0
CA C:ASP594 3.3 65.5 1.0
CB C:ASP594 3.4 66.7 1.0
C33 C:P06801 3.6 50.8 1.0
C35 C:P06801 3.6 50.6 1.0
CZ C:PHE583 3.6 58.4 1.0
CE2 C:PHE583 3.7 59.8 1.0
C14 C:P06801 3.8 55.0 1.0
C C:GLY593 3.8 62.9 1.0
C12 C:P06801 3.9 54.7 1.0
C37 C:P06801 4.1 50.4 1.0
CA C:GLY593 4.1 56.9 1.0
OD1 C:ASP594 4.2 88.2 1.0
C22 C:P06801 4.2 53.7 1.0
CG C:ASP594 4.2 83.9 1.0
S42 C:P06801 4.3 56.5 1.0
NZ C:LYS483 4.3 51.5 1.0
CD2 C:LEU514 4.3 55.2 1.0
CE C:LYS483 4.5 52.2 1.0
C17 C:P06801 4.7 53.7 1.0
S13 C:P06801 4.7 54.8 1.0
O55 C:P06801 4.8 55.2 1.0
O C:GLY593 4.8 60.3 1.0
C C:ASP594 4.8 70.1 1.0
O54 C:P06801 4.8 58.5 1.0
C2 C:P06801 4.8 55.2 1.0
C4 C:P06801 4.8 55.6 1.0
CE1 C:PHE583 4.9 59.3 1.0

Fluorine binding site 8 out of 12 in 5hie

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Fluorine binding site 8 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 8 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:68.0
occ:1.00
 F52 C:P06801 0.0 68.0 1.0
C49 C:P06801 1.4 66.0 1.0
C50 C:P06801 2.4 65.1 1.0
C43 C:P06801 2.4 63.1 1.0
O54 C:P06801 2.6 58.5 1.0
S42 C:P06801 3.1 56.5 1.0
CG2 C:ILE527 3.3 70.9 1.0
C33 C:P06801 3.5 50.8 1.0
C47 C:P06801 3.6 64.2 1.0
C46 C:P06801 3.7 64.2 1.0
CG2 C:THR529 3.8 68.3 1.0
CD1 C:ILE527 3.9 79.5 1.0
CZ C:PHE498 4.0 1.0 1.0
N40 C:P06801 4.1 51.3 1.0
C44 C:P06801 4.1 64.1 1.0
CB C:ILE527 4.2 71.4 1.0
O55 C:P06801 4.2 55.2 1.0
C31 C:P06801 4.3 51.5 1.0
C37 C:P06801 4.5 50.4 1.0
CE2 C:PHE498 4.5 0.2 1.0
CE1 C:PHE498 4.6 0.2 1.0
CG1 C:ILE527 4.6 74.1 1.0
CD C:LYS483 4.8 53.9 1.0
F53 C:P06801 4.8 64.4 1.0
CZ C:PHE468 5.0 80.5 1.0

Fluorine binding site 9 out of 12 in 5hie

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Fluorine binding site 9 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 9 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:64.4
occ:1.00
 F53 C:P06801 0.0 64.4 1.0
C46 C:P06801 1.3 64.2 1.0
C44 C:P06801 2.3 64.1 1.0
C43 C:P06801 2.4 63.1 1.0
O55 C:P06801 2.9 55.2 1.0
S42 C:P06801 3.0 56.5 1.0
CD1 C:PHE595 3.0 74.2 1.0
CE1 C:PHE595 3.1 73.5 1.0
CA C:GLY593 3.2 56.9 1.0
N40 C:P06801 3.2 51.3 1.0
C47 C:P06801 3.6 64.2 1.0
C49 C:P06801 3.7 66.0 1.0
N C:ASP594 3.8 63.8 1.0
C C:GLY593 3.8 62.9 1.0
O C:ILE592 3.9 57.9 1.0
CB C:LEU514 4.0 49.9 1.0
C50 C:P06801 4.1 65.1 1.0
CD2 C:LEU514 4.3 55.2 1.0
C31 C:P06801 4.3 51.5 1.0
CG C:PHE595 4.3 71.9 1.0
N C:GLY593 4.3 53.7 1.0
O54 C:P06801 4.4 58.5 1.0
CZ C:PHE595 4.4 72.0 1.0
C C:ILE592 4.6 55.7 1.0
N C:PHE595 4.6 68.6 1.0
CG C:LEU514 4.7 54.4 1.0
O C:LEU514 4.8 58.0 1.0
O C:GLY593 4.8 60.3 1.0
F52 C:P06801 4.8 68.0 1.0
CA C:ASP594 4.9 65.5 1.0
C33 C:P06801 4.9 50.8 1.0
CB C:PHE595 5.0 72.3 1.0
CA C:LEU514 5.0 51.1 1.0

Fluorine binding site 10 out of 12 in 5hie

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Fluorine binding site 10 out of 12 in the Braf Kinase Domain B3AC Loop Deletion 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 10 of Braf Kinase Domain B3AC Loop Deletion Mutant in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F801

b:37.9
occ:1.00
 F39 D:P06801 0.0 37.9 1.0
C32 D:P06801 1.3 37.2 1.0
C30 D:P06801 2.4 35.3 1.0
C31 D:P06801 2.4 36.9 1.0
N40 D:P06801 2.7 36.1 1.0
C16 D:P06801 2.8 34.1 1.0
N15 D:P06801 2.8 33.1 1.0
N D:ASP594 2.9 34.0 1.0
CA D:ASP594 3.3 34.6 1.0
CB D:ASP594 3.3 35.7 1.0
C35 D:P06801 3.6 33.4 1.0
C33 D:P06801 3.7 35.7 1.0
CZ D:PHE583 3.7 40.7 1.0
CE2 D:PHE583 3.8 42.8 1.0
C D:GLY593 3.8 34.9 1.0
C12 D:P06801 3.9 31.7 1.0
C14 D:P06801 3.9 30.5 1.0
CA D:GLY593 4.1 30.9 1.0
C37 D:P06801 4.1 33.3 1.0
OD1 D:ASP594 4.2 52.0 1.0
CG D:ASP594 4.2 48.2 1.0
S42 D:P06801 4.3 38.3 1.0
CD2 D:LEU514 4.4 37.1 1.0
C26 D:P06801 4.4 29.7 1.0
NZ D:LYS483 4.4 63.6 1.0
CE D:LYS483 4.6 54.0 1.0
O55 D:P06801 4.7 39.0 1.0
C4 D:P06801 4.8 32.6 1.0
C D:ASP594 4.8 38.3 1.0
O D:GLY593 4.8 32.4 1.0
O54 D:P06801 4.8 35.7 1.0
C2 D:P06801 4.8 32.8 1.0
C17 D:P06801 4.8 29.5 1.0
S13 D:P06801 4.8 27.2 1.0
CE1 D:PHE583 4.9 41.8 1.0

Reference:

S.A.Foster, D.M.Whalen, A.Ozen, M.J.Wongchenko, J.Yin, I.Yen, G.Schaefer, J.D.Mayfield, J.Chmielecki, P.J.Stephens, L.A.Albacker, Y.Yan, K.Song, G.Hatzivassiliou, C.Eigenbrot, C.Yu, A.S.Shaw, G.Manning, N.J.Skelton, S.G.Hymowitz, S.Malek. Activation Mechanism of Oncogenic Deletion Mutations in Braf, Egfr, and HER2. Cancer Cell V. 29 477 2016.
ISSN: ISSN 1535-6108
PubMed: 26996308
DOI: 10.1016/J.CCELL.2016.02.010
Page generated: Sun Dec 13 12:23:39 2020

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