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Fluorine in PDB 5jrq: BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-Vem

Enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-Vem

All present enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-Vem:
2.7.11.1;

Protein crystallography data

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-Vem, PDB code: 5jrq 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) 29.21 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.836, 67.753, 67.881, 90.00, 90.32, 90.00
R / Rfree (%) 19.5 / 25.4

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 4 in 5jrq

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Fluorine binding site 1 out of 4 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-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-6-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:22.2
occ:1.00
 F14 A:6N9801 0.0 22.2 1.0
C13 A:6N9801 1.3 19.5 1.0
H051 A:6N9801 2.2 23.3 1.0
C08 A:6N9801 2.3 19.6 1.0
C12 A:6N9801 2.4 20.0 1.0
N05 A:6N9801 2.6 19.4 1.0
C16 A:6N9801 2.9 14.6 1.0
CD1 A:LEU514 3.1 18.2 1.0
N A:ASP594 3.2 18.8 1.0
O18 A:6N9801 3.3 17.7 1.0
CA A:GLY593 3.4 17.2 1.0
CE1 A:PHE583 3.4 19.6 1.0
OD2 A:ASP594 3.5 27.5 1.0
O A:HOH928 3.6 20.8 1.0
C09 A:6N9801 3.6 20.6 1.0
C11 A:6N9801 3.6 18.7 1.0
C A:GLY593 3.7 21.7 1.0
C17 A:6N9801 3.9 17.9 1.0
CZ A:PHE583 3.9 16.4 1.0
H221 A:6N9801 4.0 19.5 1.0
CG A:ASP594 4.0 31.0 1.0
C10 A:6N9801 4.1 18.3 1.0
CA A:ASP594 4.2 19.2 1.0
S04 A:6N9801 4.2 19.9 1.0
C22 A:6N9801 4.2 16.3 1.0
H091 A:6N9801 4.4 24.7 1.0
H022 A:6N9801 4.5 24.5 1.0
CG A:LEU514 4.5 17.7 1.0
CD1 A:PHE583 4.5 18.6 1.0
NZ A:LYS483 4.5 27.5 1.0
CB A:ASP594 4.6 26.7 1.0
N A:GLY593 4.6 17.9 1.0
OD1 A:ASP594 4.7 32.8 1.0
F15 A:6N9801 4.7 16.9 1.0
O A:GLY593 4.8 17.4 1.0
O06 A:6N9801 4.8 24.1 1.0
O07 A:6N9801 4.9 24.9 1.0

Fluorine binding site 2 out of 4 in 5jrq

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Fluorine binding site 2 out of 4 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-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-6-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:16.9
occ:1.00
 F15 A:6N9801 0.0 16.9 1.0
C11 A:6N9801 1.3 18.7 1.0
C12 A:6N9801 2.3 20.0 1.0
C10 A:6N9801 2.4 18.3 1.0
H101 A:6N9801 2.6 22.0 1.0
C16 A:6N9801 2.8 14.6 1.0
C17 A:6N9801 3.1 17.9 1.0
CB A:ALA481 3.2 19.2 1.0
H221 A:6N9801 3.3 19.5 1.0
C22 A:6N9801 3.4 16.3 1.0
CG1 A:VAL471 3.5 19.6 1.0
O18 A:6N9801 3.5 17.7 1.0
C13 A:6N9801 3.6 19.5 1.0
C09 A:6N9801 3.7 20.6 1.0
N A:LYS483 3.8 15.0 1.0
C A:ALA481 3.9 14.4 1.0
C A:VAL482 3.9 14.5 1.0
N A:VAL482 4.0 14.9 1.0
CG2 A:VAL471 4.0 22.2 1.0
CB A:LYS483 4.0 18.9 1.0
C08 A:6N9801 4.1 19.6 1.0
CA A:ALA481 4.1 16.4 1.0
C19 A:6N9801 4.2 14.1 1.0
OG1 A:THR529 4.2 17.6 1.0
O A:VAL482 4.3 18.8 1.0
CA A:LYS483 4.3 18.4 1.0
O A:ALA481 4.3 17.9 1.0
CB A:VAL471 4.3 24.5 1.0
CA A:VAL482 4.4 14.7 1.0
N21 A:6N9801 4.4 19.8 1.0
H091 A:6N9801 4.5 24.7 1.0
F14 A:6N9801 4.7 22.2 1.0
C20 A:6N9801 4.8 18.5 1.0
O A:ILE527 4.9 14.5 1.0
CA A:VAL471 4.9 22.8 1.0

Fluorine binding site 3 out of 4 in 5jrq

Go back to Fluorine Binding Sites List in 5jrq
Fluorine binding site 3 out of 4 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-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-6-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:24.2
occ:1.00
 F14 B:6N9801 0.0 24.2 1.0
C13 B:6N9801 1.3 16.9 1.0
H051 B:6N9801 2.2 26.0 1.0
C08 B:6N9801 2.3 18.4 1.0
C12 B:6N9801 2.4 15.9 1.0
N05 B:6N9801 2.6 21.7 1.0
C16 B:6N9801 2.8 17.4 1.0
CD2 B:LEU514 3.1 17.9 1.0
O18 B:6N9801 3.2 14.4 1.0
OD2 B:ASP594 3.2 34.0 1.0
N B:ASP594 3.3 22.6 1.0
CE1 B:PHE583 3.4 18.5 1.0
O B:HOH917 3.5 19.1 1.0
C09 B:6N9801 3.6 21.2 1.0
CA B:GLY593 3.6 19.3 1.0
C11 B:6N9801 3.6 18.4 1.0
CZ B:PHE583 3.7 16.4 1.0
C17 B:6N9801 3.8 17.6 1.0
C B:GLY593 3.8 22.3 1.0
H221 B:6N9801 4.0 17.9 1.0
CG B:ASP594 4.1 34.5 1.0
C10 B:6N9801 4.1 18.8 1.0
CA B:ASP594 4.2 22.3 1.0
C22 B:6N9801 4.2 14.9 1.0
S04 B:6N9801 4.2 24.0 1.0
H091 B:6N9801 4.4 25.4 1.0
NZ B:LYS483 4.5 28.0 1.0
CB B:ASP594 4.5 21.4 1.0
CD1 B:PHE583 4.5 15.2 1.0
CG B:LEU514 4.6 26.1 1.0
CE B:LYS483 4.7 29.4 1.0
H022 B:6N9801 4.7 29.2 1.0
F15 B:6N9801 4.8 17.2 1.0
O06 B:6N9801 4.8 29.5 1.0
N B:GLY593 4.8 20.6 1.0
CE2 B:PHE583 4.9 15.5 1.0
O07 B:6N9801 4.9 26.7 1.0
O B:GLY593 4.9 19.2 1.0
OD1 B:ASP594 4.9 37.2 1.0
C19 B:6N9801 5.0 14.5 1.0

Fluorine binding site 4 out of 4 in 5jrq

Go back to Fluorine Binding Sites List in 5jrq
Fluorine binding site 4 out of 4 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-6-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-6-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:17.2
occ:1.00
 F15 B:6N9801 0.0 17.2 1.0
C11 B:6N9801 1.3 18.4 1.0
C12 B:6N9801 2.4 15.9 1.0
C10 B:6N9801 2.4 18.8 1.0
H101 B:6N9801 2.6 22.5 1.0
C16 B:6N9801 2.9 17.4 1.0
CB B:ALA481 3.2 15.5 1.0
H221 B:6N9801 3.3 17.9 1.0
C17 B:6N9801 3.3 17.6 1.0
C22 B:6N9801 3.4 14.9 1.0
CG1 B:VAL471 3.5 22.6 1.0
N B:LYS483 3.6 16.8 1.0
C13 B:6N9801 3.6 16.9 1.0
C09 B:6N9801 3.7 21.2 1.0
C B:ALA481 3.7 15.6 1.0
O18 B:6N9801 3.7 14.4 1.0
N B:VAL482 3.7 14.5 1.0
C B:VAL482 3.7 14.9 1.0
CG2 B:VAL471 3.8 17.8 1.0
CB B:LYS483 3.9 18.8 1.0
O B:ALA481 4.0 17.1 1.0
CA B:ALA481 4.0 14.5 1.0
CA B:LYS483 4.1 21.4 1.0
C08 B:6N9801 4.1 18.4 1.0
O B:VAL482 4.1 19.6 1.0
CA B:VAL482 4.1 17.4 1.0
OG1 B:THR529 4.2 22.9 1.0
CB B:VAL471 4.2 20.1 1.0
C19 B:6N9801 4.3 14.5 1.0
N21 B:6N9801 4.5 15.5 1.0
H091 B:6N9801 4.5 25.4 1.0
O B:ILE527 4.7 16.2 1.0
F14 B:6N9801 4.8 24.2 1.0
CA B:VAL471 4.9 21.4 1.0
C20 B:6N9801 4.9 19.2 1.0
O B:TYR472 5.0 18.9 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 10:37:53 2024

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