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Fluorine in PDB 5jsm: BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem

Enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem

All present enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem:
2.7.11.1;

Protein crystallography data

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem, PDB code: 5jsm was solved by M.J.Grasso, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.91 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.608, 68.258, 276.007, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26

Other elements in 5jsm:

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem (pdb code 5jsm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem, PDB code: 5jsm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5jsm

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Fluorine binding site 1 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:34.2
occ:1.00
 F01 B:6NB801 0.0 34.2 1.0
C20 B:6NB801 1.4 31.1 1.0
C15 B:6NB801 2.4 31.9 1.0
C19 B:6NB801 2.4 34.5 1.0
N03 B:6NB801 2.7 34.5 1.0
C14 B:6NB801 2.8 34.6 1.0
O01 B:6NB801 3.1 35.0 1.0
O B:HOH926 3.1 44.4 1.0
N B:ASP594 3.3 34.6 1.0
CD1 B:LEU514 3.3 27.0 1.0
CE1 B:PHE583 3.4 37.2 1.0
OD2 B:ASP594 3.4 45.1 1.0
CA B:GLY593 3.6 30.4 1.0
C16 B:6NB801 3.6 28.4 1.0
C18 B:6NB801 3.7 32.6 1.0
C12 B:6NB801 3.7 33.8 1.0
C B:GLY593 3.8 28.2 1.0
CZ B:PHE583 3.8 37.1 1.0
C17 B:6NB801 4.2 37.0 1.0
C13 B:6NB801 4.2 36.0 1.0
CA B:ASP594 4.3 37.8 1.0
CG B:ASP594 4.3 52.7 1.0
S01 B:6NB801 4.4 37.6 1.0
CD1 B:PHE583 4.5 33.9 1.0
CB B:ASP594 4.6 40.2 1.0
F02 B:6NB801 4.7 34.5 1.0
CG B:LEU514 4.7 35.4 1.0
N B:GLY593 4.8 23.9 1.0
O B:GLY593 4.8 30.6 1.0
H22 B:DMS802 4.8 76.8 1.0
O03 B:6NB801 4.9 34.4 1.0
C09 B:6NB801 4.9 35.5 1.0

Fluorine binding site 2 out of 8 in 5jsm

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Fluorine binding site 2 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:34.5
occ:1.00
 F02 B:6NB801 0.0 34.5 1.0
C16 B:6NB801 1.3 28.4 1.0
C15 B:6NB801 2.3 31.9 1.0
C17 B:6NB801 2.4 37.0 1.0
C14 B:6NB801 2.8 34.6 1.0
CB B:ALA481 3.1 31.2 1.0
C12 B:6NB801 3.2 33.8 1.0
C13 B:6NB801 3.5 36.0 1.0
CG1 B:VAL471 3.5 41.8 1.0
O01 B:6NB801 3.6 35.0 1.0
C20 B:6NB801 3.6 31.1 1.0
C18 B:6NB801 3.7 32.6 1.0
CG2 B:VAL471 3.7 35.6 1.0
C B:ALA481 3.8 34.9 1.0
N B:VAL482 4.0 30.9 1.0
N B:LYS483 4.0 37.3 1.0
CB B:LYS483 4.0 30.3 1.0
CA B:ALA481 4.1 26.9 1.0
C B:VAL482 4.1 38.0 1.0
C19 B:6NB801 4.1 34.5 1.0
O B:ALA481 4.1 37.8 1.0
CB B:VAL471 4.2 37.4 1.0
C09 B:6NB801 4.3 35.5 1.0
O B:VAL482 4.4 39.4 1.0
CA B:LYS483 4.4 36.1 1.0
CA B:VAL482 4.5 39.5 1.0
N02 B:6NB801 4.5 33.3 1.0
CG2 B:THR529 4.7 30.0 1.0
CB B:THR529 4.7 38.9 1.0
F01 B:6NB801 4.7 34.2 1.0
O B:ILE527 4.8 32.1 1.0
CA B:VAL471 4.8 42.4 1.0
C10 B:6NB801 4.9 33.7 1.0

Fluorine binding site 3 out of 8 in 5jsm

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Fluorine binding site 3 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:28.8
occ:1.00
 F03 B:6NB801 0.0 28.8 1.0
C49 B:6NB801 1.3 25.0 1.0
C44 B:6NB801 2.3 26.0 1.0
C48 B:6NB801 2.3 28.6 1.0
N B:6NB801 2.7 26.7 1.0
C43 B:6NB801 2.7 24.2 1.0
O08 B:6NB801 2.9 23.7 1.0
CE1 A:PHE583 3.2 26.7 1.0
CD1 A:LEU514 3.3 23.8 1.0
N A:ASP594 3.4 29.6 1.0
O A:HOH927 3.5 34.3 1.0
OD2 A:ASP594 3.6 38.9 1.0
C45 B:6NB801 3.6 30.0 1.0
CA A:GLY593 3.6 26.1 1.0
C47 B:6NB801 3.6 32.3 1.0
CZ A:PHE583 3.6 33.2 1.0
C41 B:6NB801 3.7 27.1 1.0
C A:GLY593 3.8 26.4 1.0
C46 B:6NB801 4.1 29.5 1.0
C42 B:6NB801 4.2 35.1 1.0
CA A:ASP594 4.3 30.0 1.0
CD1 A:PHE583 4.3 33.9 1.0
S B:6NB801 4.4 31.8 1.0
CG A:ASP594 4.4 40.0 1.0
NZ A:LYS483 4.6 38.7 1.0
CB A:ASP594 4.6 37.3 1.0
F B:6NB801 4.7 27.8 1.0
N A:GLY593 4.7 28.6 1.0
CG A:LEU514 4.7 27.8 1.0
O A:GLY593 4.8 27.5 1.0
C38 B:6NB801 4.9 30.6 1.0
O09 B:6NB801 4.9 32.0 1.0
CE2 A:PHE583 5.0 30.5 1.0

Fluorine binding site 4 out of 8 in 5jsm

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Fluorine binding site 4 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:27.8
occ:1.00
 F B:6NB801 0.0 27.8 1.0
C45 B:6NB801 1.4 30.0 1.0
C44 B:6NB801 2.3 26.0 1.0
C46 B:6NB801 2.4 29.5 1.0
C43 B:6NB801 2.9 24.2 1.0
C41 B:6NB801 3.3 27.1 1.0
CB A:ALA481 3.3 26.2 1.0
C42 B:6NB801 3.5 35.1 1.0
CG1 A:VAL471 3.5 26.0 1.0
C49 B:6NB801 3.6 25.0 1.0
C47 B:6NB801 3.6 32.3 1.0
O08 B:6NB801 3.7 23.7 1.0
CB A:LYS483 3.7 33.7 1.0
N A:LYS483 3.8 29.7 1.0
C A:ALA481 3.8 27.7 1.0
N A:VAL482 3.9 27.1 1.0
C A:VAL482 3.9 32.8 1.0
O A:ALA481 4.1 28.2 1.0
C48 B:6NB801 4.1 28.6 1.0
CG2 A:VAL471 4.1 35.4 1.0
CA A:ALA481 4.2 25.4 1.0
CA A:LYS483 4.2 29.7 1.0
O A:VAL482 4.2 31.4 1.0
C38 B:6NB801 4.3 30.6 1.0
CA A:VAL482 4.3 32.7 1.0
OG1 A:THR529 4.3 35.4 1.0
CB A:VAL471 4.4 32.3 1.0
N05 B:6NB801 4.5 25.6 1.0
O A:ILE527 4.7 29.2 1.0
F03 B:6NB801 4.7 28.8 1.0
CG2 A:THR529 4.8 36.5 1.0
CA A:VAL471 4.9 31.9 1.0
C39 B:6NB801 4.9 28.6 1.0

Fluorine binding site 5 out of 8 in 5jsm

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Fluorine binding site 5 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:37.7
occ:1.00
 F01 C:6NB801 0.0 37.7 1.0
C20 C:6NB801 1.4 32.5 1.0
C15 C:6NB801 2.4 38.0 1.0
C19 C:6NB801 2.4 38.1 1.0
N03 C:6NB801 2.8 35.5 1.0
C14 C:6NB801 2.8 34.9 1.0
O01 C:6NB801 3.1 33.7 1.0
CD1 D:LEU514 3.2 27.9 1.0
CE1 D:PHE583 3.2 29.4 1.0
N D:ASP594 3.3 32.0 1.0
O D:HOH929 3.4 41.0 1.0
CA D:GLY593 3.6 34.9 1.0
CZ D:PHE583 3.6 37.7 1.0
C16 C:6NB801 3.7 36.7 1.0
C18 C:6NB801 3.7 37.4 1.0
C12 C:6NB801 3.7 33.4 1.0
C D:GLY593 3.7 37.1 1.0
OD2 D:ASP594 3.8 58.9 1.0
C13 C:6NB801 4.2 37.1 1.0
C17 C:6NB801 4.2 38.8 1.0
CA D:ASP594 4.3 43.2 1.0
CD1 D:PHE583 4.4 35.1 1.0
S01 C:6NB801 4.4 36.9 1.0
CG D:ASP594 4.5 61.0 1.0
CG D:LEU514 4.6 34.4 1.0
CB D:ASP594 4.6 46.3 1.0
N D:GLY593 4.6 29.0 1.0
NZ D:LYS483 4.7 44.1 1.0
F02 C:6NB801 4.7 34.2 1.0
O D:GLY593 4.8 32.1 1.0
CE2 D:PHE583 4.9 34.4 1.0
C09 C:6NB801 4.9 34.1 1.0

Fluorine binding site 6 out of 8 in 5jsm

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Fluorine binding site 6 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:34.2
occ:1.00
 F02 C:6NB801 0.0 34.2 1.0
C16 C:6NB801 1.3 36.7 1.0
C15 C:6NB801 2.3 38.0 1.0
C17 C:6NB801 2.4 38.8 1.0
C14 C:6NB801 2.8 34.9 1.0
CB D:ALA481 3.1 30.7 1.0
C12 C:6NB801 3.3 33.4 1.0
O01 C:6NB801 3.6 33.7 1.0
C13 C:6NB801 3.6 37.1 1.0
C20 C:6NB801 3.6 32.5 1.0
C18 C:6NB801 3.7 37.4 1.0
CG1 D:VAL471 3.7 39.6 1.0
CG2 D:VAL471 3.7 37.7 1.0
C D:ALA481 3.9 34.3 1.0
CB D:LYS483 4.0 35.7 1.0
N D:LYS483 4.0 34.0 1.0
N D:VAL482 4.0 34.2 1.0
C D:VAL482 4.0 36.0 1.0
CA D:ALA481 4.1 29.8 1.0
C19 C:6NB801 4.1 38.1 1.0
OG1 D:THR529 4.2 36.6 1.0
CB D:VAL471 4.2 37.8 1.0
O D:ALA481 4.2 37.9 1.0
O D:VAL482 4.3 36.5 1.0
C09 C:6NB801 4.3 34.1 1.0
CA D:LYS483 4.4 35.3 1.0
CA D:VAL482 4.5 37.6 1.0
N02 C:6NB801 4.6 28.9 1.0
F01 C:6NB801 4.7 37.7 1.0
O D:ILE527 4.7 29.0 1.0
CA D:VAL471 4.8 37.3 1.0
CG2 D:THR529 5.0 35.6 1.0
C10 C:6NB801 5.0 33.5 1.0

Fluorine binding site 7 out of 8 in 5jsm

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Fluorine binding site 7 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:30.1
occ:1.00
 F03 C:6NB801 0.0 30.1 1.0
C49 C:6NB801 1.3 32.0 1.0
C48 C:6NB801 2.3 30.9 1.0
C44 C:6NB801 2.3 32.3 1.0
N C:6NB801 2.7 28.4 1.0
C43 C:6NB801 2.8 31.4 1.0
O08 C:6NB801 3.1 34.7 1.0
CE1 C:PHE583 3.2 32.6 1.0
OD2 C:ASP594 3.3 49.3 1.0
N C:ASP594 3.3 35.7 1.0
O C:HOH917 3.4 44.4 1.0
CD1 C:LEU514 3.4 26.5 1.0
CA C:GLY593 3.5 34.2 1.0
C45 C:6NB801 3.6 32.3 1.0
C47 C:6NB801 3.6 35.9 1.0
CZ C:PHE583 3.7 37.0 1.0
C41 C:6NB801 3.8 30.6 1.0
C C:GLY593 3.8 35.8 1.0
C46 C:6NB801 4.1 35.7 1.0
C42 C:6NB801 4.2 32.9 1.0
CG C:ASP594 4.2 51.7 1.0
CD1 C:PHE583 4.3 40.7 1.0
CA C:ASP594 4.3 36.2 1.0
S C:6NB801 4.3 37.7 1.0
NZ C:LYS483 4.5 45.8 1.0
N C:GLY593 4.6 34.3 1.0
CB C:ASP594 4.6 44.3 1.0
F C:6NB801 4.7 33.8 1.0
CG C:LEU514 4.8 33.3 1.0
O C:GLY593 4.9 36.5 1.0
O09 C:6NB801 4.9 34.4 1.0
C38 C:6NB801 5.0 35.2 1.0

Fluorine binding site 8 out of 8 in 5jsm

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Fluorine binding site 8 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:33.8
occ:1.00
 F C:6NB801 0.0 33.8 1.0
C45 C:6NB801 1.4 32.3 1.0
C44 C:6NB801 2.4 32.3 1.0
C46 C:6NB801 2.4 35.7 1.0
C43 C:6NB801 2.8 31.4 1.0
C41 C:6NB801 3.2 30.6 1.0
CB C:ALA481 3.4 26.1 1.0
C42 C:6NB801 3.4 32.9 1.0
CG1 C:VAL471 3.5 29.1 1.0
O08 C:6NB801 3.6 34.7 1.0
C49 C:6NB801 3.6 32.0 1.0
C47 C:6NB801 3.7 35.9 1.0
N C:LYS483 3.8 34.4 1.0
CB C:LYS483 3.8 30.8 1.0
C C:ALA481 3.8 35.6 1.0
CG2 C:VAL471 3.9 35.9 1.0
N C:VAL482 3.9 34.5 1.0
C C:VAL482 3.9 39.5 1.0
O C:ALA481 4.1 33.3 1.0
C48 C:6NB801 4.1 30.9 1.0
OG1 C:THR529 4.1 31.9 1.0
CA C:ALA481 4.2 25.9 1.0
C38 C:6NB801 4.2 35.2 1.0
CB C:VAL471 4.3 37.5 1.0
CA C:LYS483 4.3 35.2 1.0
CA C:VAL482 4.3 34.6 1.0
O C:VAL482 4.4 38.8 1.0
N05 C:6NB801 4.4 34.2 1.0
F03 C:6NB801 4.7 30.1 1.0
O C:ILE527 4.7 31.9 1.0
C39 C:6NB801 4.8 30.8 1.0
CA C:VAL471 4.9 33.0 1.0

Reference:

M.Grasso, M.A.Estrada, C.Ventocilla, M.Samanta, J.Maksimoska, J.Villanueva, J.D.Winkler, R.Marmorstein. Chemically Linked Vemurafenib Inhibitors Promote An Inactive Braf(V600E) Conformation. Acs Chem.Biol. V. 11 2876 2016.
ISSN: ESSN 1554-8937
PubMed: 27571413
DOI: 10.1021/ACSCHEMBIO.6B00529
Page generated: Thu Aug 1 10:39:18 2024

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