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Fluorine in PDB 5jt2: BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide

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

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

Protein crystallography data

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide, PDB code: 5jt2 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) 29.59 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.102, 68.442, 275.603, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide (pdb code 5jt2). 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-Bisamide, PDB code: 5jt2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:21.4
occ:1.00
 F14 A:6NC802 0.0 21.4 1.0
C13 A:6NC802 1.3 20.9 1.0
C12 A:6NC802 2.4 22.1 1.0
C08 A:6NC802 2.4 21.8 1.0
H051 A:6NC802 2.5 30.8 1.0
N05 A:6NC802 2.7 25.7 1.0
C16 A:6NC802 2.7 22.6 1.0
O18 A:6NC802 2.9 20.0 1.0
CE1 B:PHE583 3.2 21.0 1.0
CD1 B:LEU514 3.4 20.7 1.0
CA B:GLY593 3.5 14.9 1.0
C11 A:6NC802 3.6 23.1 1.0
N B:ASP594 3.6 21.5 1.0
C09 A:6NC802 3.6 23.2 1.0
OD2 B:ASP594 3.7 24.0 1.0
CZ B:PHE583 3.7 20.5 1.0
C17 A:6NC802 3.8 22.6 1.0
C B:GLY593 3.9 22.2 1.0
H221 A:6NC802 4.0 29.2 1.0
C10 A:6NC802 4.1 22.6 1.0
C22 A:6NC802 4.2 24.3 1.0
CD1 B:PHE583 4.3 24.6 1.0
H091 A:6NC802 4.4 27.8 1.0
S04 A:6NC802 4.4 24.5 1.0
H032 A:6NC802 4.4 22.7 1.0
N B:GLY593 4.6 16.9 1.0
CG B:ASP594 4.6 30.8 1.0
NZ B:LYS483 4.7 25.1 1.0
CA B:ASP594 4.7 19.6 1.0
F15 A:6NC802 4.7 26.8 1.0
CG B:LEU514 4.8 26.6 1.0
CB B:ASN581 4.9 24.3 1.0
C19 A:6NC802 4.9 23.0 1.0
CE2 B:PHE583 5.0 26.0 1.0

Fluorine binding site 2 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:26.8
occ:1.00
 F15 A:6NC802 0.0 26.8 1.0
C11 A:6NC802 1.3 23.1 1.0
C10 A:6NC802 2.3 22.6 1.0
C12 A:6NC802 2.4 22.1 1.0
H101 A:6NC802 2.5 27.1 1.0
C16 A:6NC802 3.0 22.6 1.0
H221 A:6NC802 3.2 29.2 1.0
C17 A:6NC802 3.4 22.6 1.0
CB B:ALA481 3.4 23.9 1.0
C22 A:6NC802 3.4 24.3 1.0
C09 A:6NC802 3.6 23.2 1.0
C13 A:6NC802 3.6 20.9 1.0
N B:LYS483 3.7 31.1 1.0
CG1 B:VAL471 3.7 21.9 1.0
C B:ALA481 3.8 25.8 1.0
O18 A:6NC802 3.8 20.0 1.0
N B:VAL482 3.8 25.8 1.0
CG2 B:VAL471 3.8 27.5 1.0
C B:VAL482 3.9 25.6 1.0
CB B:LYS483 4.0 30.2 1.0
O B:ALA481 4.0 26.3 1.0
C08 A:6NC802 4.1 21.8 1.0
CA B:VAL482 4.2 22.8 1.0
CA B:ALA481 4.2 22.9 1.0
OG1 B:THR529 4.3 28.7 1.0
CA B:LYS483 4.3 30.8 1.0
H091 A:6NC802 4.3 27.8 1.0
CB B:VAL471 4.3 28.0 1.0
O B:VAL482 4.4 29.1 1.0
C19 A:6NC802 4.5 23.0 1.0
N21 A:6NC802 4.5 30.7 1.0
O B:ILE527 4.5 24.5 1.0
F14 A:6NC802 4.7 21.4 1.0
CA B:VAL471 5.0 29.6 1.0
C20 A:6NC802 5.0 26.3 1.0

Fluorine binding site 3 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 3 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:20.9
occ:1.00
 F55 A:6NC802 0.0 20.9 1.0
C54 A:6NC802 1.4 23.1 1.0
H461 A:6NC802 2.3 37.5 1.0
C49 A:6NC802 2.4 28.3 1.0
C53 A:6NC802 2.4 25.9 1.0
N46 A:6NC802 2.7 31.2 1.0
C57 A:6NC802 2.8 29.2 1.0
O59 A:6NC802 3.2 26.9 1.0
CE1 A:PHE583 3.2 26.6 1.0
CD1 A:LEU514 3.3 18.2 1.0
OD2 A:ASP594 3.5 42.5 1.0
CA A:GLY593 3.5 23.9 1.0
N A:ASP594 3.6 25.8 1.0
C50 A:6NC802 3.6 27.9 1.0
C52 A:6NC802 3.6 23.2 1.0
CZ A:PHE583 3.8 23.6 1.0
C58 A:6NC802 3.8 24.5 1.0
C A:GLY593 3.9 25.7 1.0
H631 A:6NC802 4.1 27.0 1.0
CD1 A:PHE583 4.1 29.2 1.0
C51 A:6NC802 4.1 29.8 1.0
C63 A:6NC802 4.3 22.5 1.0
S45 A:6NC802 4.3 30.3 1.0
H501 A:6NC802 4.4 33.5 1.0
CG A:ASP594 4.5 42.4 1.0
N A:GLY593 4.6 23.3 1.0
CA A:ASP594 4.7 29.9 1.0
CG A:LEU514 4.7 25.0 1.0
F56 A:6NC802 4.8 23.2 1.0
O A:GLY593 5.0 21.5 1.0
C60 A:6NC802 5.0 25.4 1.0
CB A:ASP594 5.0 32.5 1.0

Fluorine binding site 4 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:23.2
occ:1.00
 F56 A:6NC802 0.0 23.2 1.0
C52 A:6NC802 1.4 23.2 1.0
C53 A:6NC802 2.4 25.9 1.0
C51 A:6NC802 2.4 29.8 1.0
H511 A:6NC802 2.6 35.7 1.0
C57 A:6NC802 2.8 29.2 1.0
CB A:ALA481 3.0 21.1 1.0
C58 A:6NC802 3.3 24.5 1.0
H631 A:6NC802 3.4 27.0 1.0
CG1 A:VAL471 3.5 27.6 1.0
C63 A:6NC802 3.5 22.5 1.0
O59 A:6NC802 3.6 26.9 1.0
C A:ALA481 3.6 25.1 1.0
C54 A:6NC802 3.7 23.1 1.0
C50 A:6NC802 3.7 27.9 1.0
N A:VAL482 3.7 25.6 1.0
CG2 A:VAL471 3.9 29.5 1.0
CA A:ALA481 3.9 22.5 1.0
C A:VAL482 4.0 28.5 1.0
O A:ALA481 4.0 26.0 1.0
N A:LYS483 4.1 26.4 1.0
C49 A:6NC802 4.1 28.3 1.0
CB A:VAL471 4.2 31.5 1.0
OG1 A:THR529 4.3 29.1 1.0
C60 A:6NC802 4.3 25.4 1.0
O A:VAL482 4.3 29.0 1.0
CA A:VAL482 4.3 24.7 1.0
CB A:LYS483 4.3 27.3 1.0
H501 A:6NC802 4.4 33.5 1.0
N62 A:6NC802 4.5 25.4 1.0
CA A:LYS483 4.6 24.9 1.0
F55 A:6NC802 4.8 20.9 1.0
CA A:VAL471 4.8 32.9 1.0
O A:ILE527 4.9 24.9 1.0
C61 A:6NC802 4.9 25.8 1.0

Fluorine binding site 5 out of 8 in 5jt2

Go back to Fluorine Binding Sites List in 5jt2
Fluorine binding site 5 out of 8 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-Bisamide


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:28.2
occ:1.00
 F14 C:6NC801 0.0 28.2 1.0
C13 C:6NC801 1.3 28.4 1.0
C08 C:6NC801 2.4 27.5 1.0
H051 C:6NC801 2.4 32.5 1.0
C12 C:6NC801 2.4 26.1 1.0
N05 C:6NC801 2.7 27.1 1.0
C16 C:6NC801 2.9 25.9 1.0
O18 C:6NC801 3.1 28.5 1.0
OD2 D:ASP594 3.2 37.4 1.0
N D:ASP594 3.2 28.8 1.0
CE1 D:PHE583 3.3 28.8 1.0
CA D:GLY593 3.5 23.9 1.0
CD1 D:LEU514 3.6 22.0 1.0
C09 C:6NC801 3.6 26.6 1.0
C11 C:6NC801 3.6 26.5 1.0
C D:GLY593 3.7 28.9 1.0
CZ D:PHE583 3.8 26.3 1.0
C17 C:6NC801 3.9 27.3 1.0
CG D:ASP594 4.1 40.9 1.0
H221 C:6NC801 4.1 33.1 1.0
C10 C:6NC801 4.1 26.4 1.0
CA D:ASP594 4.2 31.9 1.0
CD1 D:PHE583 4.3 29.4 1.0
C22 C:6NC801 4.3 27.6 1.0
S04 C:6NC801 4.3 26.4 1.0
H091 C:6NC801 4.4 31.9 1.0
CB D:ASP594 4.5 37.9 1.0
NZ D:LYS483 4.5 35.7 1.0
H032 C:6NC801 4.6 26.2 1.0
N D:GLY593 4.6 27.9 1.0
H031 C:6NC801 4.7 26.2 1.0
O D:GLY593 4.7 30.7 1.0
F15 C:6NC801 4.7 26.4 1.0
C03 C:6NC801 4.8 21.8 1.0
CB D:ASN581 4.9 38.5 1.0
CG D:LEU514 4.9 26.2 1.0

Fluorine binding site 6 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:26.4
occ:1.00
 F15 C:6NC801 0.0 26.4 1.0
C11 C:6NC801 1.3 26.5 1.0
C12 C:6NC801 2.4 26.1 1.0
C10 C:6NC801 2.4 26.4 1.0
H101 C:6NC801 2.6 31.6 1.0
C16 C:6NC801 2.8 25.9 1.0
C17 C:6NC801 3.1 27.3 1.0
H221 C:6NC801 3.2 33.1 1.0
CB D:ALA481 3.2 25.0 1.0
C22 C:6NC801 3.3 27.6 1.0
O18 C:6NC801 3.6 28.5 1.0
C13 C:6NC801 3.6 28.4 1.0
C09 C:6NC801 3.6 26.6 1.0
CG1 D:VAL471 3.7 28.6 1.0
C D:ALA481 3.8 31.5 1.0
N D:VAL482 3.9 30.8 1.0
N D:LYS483 4.0 28.9 1.0
CG2 D:VAL471 4.0 27.5 1.0
C D:VAL482 4.1 29.5 1.0
CB D:LYS483 4.1 30.0 1.0
CA D:ALA481 4.1 26.0 1.0
C08 C:6NC801 4.1 27.5 1.0
OG1 D:THR529 4.1 28.3 1.0
O D:ALA481 4.2 30.2 1.0
C19 C:6NC801 4.2 26.2 1.0
N21 C:6NC801 4.3 31.2 1.0
CB D:VAL471 4.4 27.0 1.0
H091 C:6NC801 4.4 31.9 1.0
O D:VAL482 4.4 33.9 1.0
CA D:VAL482 4.4 26.0 1.0
CA D:LYS483 4.5 26.5 1.0
F14 C:6NC801 4.7 28.2 1.0
C20 C:6NC801 4.7 30.2 1.0
O D:ILE527 4.8 30.4 1.0
CG2 D:THR529 4.9 25.4 1.0

Fluorine binding site 7 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:30.7
occ:1.00
 F55 C:6NC801 0.0 30.7 1.0
C54 C:6NC801 1.4 34.6 1.0
H461 C:6NC801 2.3 43.2 1.0
C49 C:6NC801 2.4 36.7 1.0
C53 C:6NC801 2.4 34.8 1.0
N46 C:6NC801 2.6 36.0 1.0
C57 C:6NC801 2.8 38.2 1.0
CD1 C:LEU514 3.0 27.5 1.0
CE1 C:PHE583 3.2 29.1 1.0
O59 C:6NC801 3.2 39.2 1.0
CA C:GLY593 3.3 32.8 1.0
N C:ASP594 3.5 31.9 1.0
C50 C:6NC801 3.6 37.9 1.0
C52 C:6NC801 3.6 31.8 1.0
O C:HOH902 3.7 37.8 1.0
C C:GLY593 3.7 33.3 1.0
CZ C:PHE583 3.8 27.0 1.0
C58 C:6NC801 3.8 30.1 1.0
H631 C:6NC801 3.9 37.3 1.0
OD2 C:ASP594 4.0 49.2 1.0
CD1 C:PHE583 4.1 26.9 1.0
C51 C:6NC801 4.1 33.4 1.0
C63 C:6NC801 4.2 31.1 1.0
S45 C:6NC801 4.3 34.0 1.0
CG C:LEU514 4.4 32.5 1.0
H501 C:6NC801 4.4 45.5 1.0
N C:GLY593 4.4 29.5 1.0
CA C:ASP594 4.6 38.1 1.0
NZ C:LYS483 4.8 45.3 1.0
F56 C:6NC801 4.8 30.2 1.0
O C:GLY593 4.8 35.8 1.0
CG C:ASP594 4.9 48.8 1.0
C60 C:6NC801 4.9 32.4 1.0
H432 C:6NC801 5.0 38.0 1.0
O47 C:6NC801 5.0 31.0 1.0
CE2 C:PHE583 5.0 32.7 1.0
H442 C:6NC801 5.0 42.9 1.0

Fluorine binding site 8 out of 8 in 5jt2

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


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-Bisamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:30.2
occ:1.00
 F56 C:6NC801 0.0 30.2 1.0
C52 C:6NC801 1.4 31.8 1.0
C53 C:6NC801 2.4 34.8 1.0
C51 C:6NC801 2.4 33.4 1.0
H511 C:6NC801 2.6 40.1 1.0
C57 C:6NC801 2.9 38.2 1.0
CB C:ALA481 3.2 24.7 1.0
CG2 C:VAL471 3.4 44.8 1.0
CG1 C:VAL471 3.4 31.2 1.0
C58 C:6NC801 3.4 30.1 1.0
O59 C:6NC801 3.5 39.2 1.0
C54 C:6NC801 3.7 34.6 1.0
H631 C:6NC801 3.7 37.3 1.0
C50 C:6NC801 3.7 37.9 1.0
C63 C:6NC801 3.8 31.1 1.0
C C:ALA481 3.9 32.6 1.0
CB C:VAL471 3.9 38.4 1.0
N C:VAL482 4.0 29.6 1.0
N C:LYS483 4.0 30.3 1.0
CB C:LYS483 4.1 39.3 1.0
C C:VAL482 4.1 34.4 1.0
CA C:ALA481 4.1 24.4 1.0
O C:ALA481 4.1 26.8 1.0
C49 C:6NC801 4.1 36.7 1.0
CA C:LYS483 4.4 35.5 1.0
C60 C:6NC801 4.4 32.4 1.0
OG1 C:THR529 4.4 32.1 1.0
H501 C:6NC801 4.4 45.5 1.0
CA C:VAL482 4.5 31.7 1.0
O C:VAL482 4.5 35.6 1.0
CA C:VAL471 4.6 36.3 1.0
N62 C:6NC801 4.8 31.7 1.0
F55 C:6NC801 4.8 30.7 1.0
O C:ILE527 4.9 29.1 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 10:40:18 2024

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