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Fluorine in PDB 6bu6: Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor

Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor

All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor, PDB code: 6bu6 was solved by R.M.Counago, C.V.Dos Reis, G.P.De Souza, A.S.Santiago, A.Azevedo, C.Guimaraes, A.Mascarello, F.Gama, M.Ferreira, K.B.Massirer, P.Arruda, A.M.Edwards, J.M.Elkins, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.215, 96.572, 193.056, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.3

Other elements in 6bu6:

The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor (pdb code 6bu6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor, PDB code: 6bu6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6bu6

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Fluorine binding site 1 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:51.1
occ:1.00
 F1 A:E8V401 0.0 51.1 1.0
C9 A:E8V401 1.4 49.7 1.0
C8 A:E8V401 2.4 47.9 1.0
C10 A:E8V401 2.4 49.9 1.0
CE A:MET131 2.7 23.1 0.5
O1 A:E8V401 2.8 48.1 1.0
O A:HOH501 2.9 27.2 1.0
CB A:VAL196 3.1 24.4 1.0
CG1 A:VAL196 3.1 24.7 1.0
SD A:MET131 3.5 24.3 0.5
C11 A:E8V401 3.6 54.8 1.0
OH A:TYR87 3.6 25.8 1.0
C6 A:E8V401 3.6 43.7 1.0
CG A:PRO111 4.0 22.9 1.0
CA A:VAL196 4.1 22.3 1.0
C12 A:E8V401 4.1 50.3 1.0
CG2 A:VAL196 4.1 26.0 1.0
CE2 A:PHE134 4.3 32.7 1.0
N A:ASP197 4.5 21.9 1.0
CB A:PRO111 4.5 23.4 1.0
CD2 A:PHE134 4.6 32.8 1.0
F2 A:E8V401 4.7 57.9 1.0
CZ A:TYR87 4.8 25.8 1.0
CD1 A:LEU184 4.8 29.1 1.0
N2 A:E8V401 4.8 42.5 1.0
C1 A:E8V401 4.9 42.8 1.0
C A:VAL196 4.9 23.2 1.0
O A:HOH529 4.9 58.7 1.0
CG A:MET131 4.9 25.6 0.5

Fluorine binding site 2 out of 12 in 6bu6

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Fluorine binding site 2 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:57.9
occ:1.00
 F2 A:E8V401 0.0 57.9 1.0
C11 A:E8V401 1.4 54.8 1.0
C10 A:E8V401 2.3 49.9 1.0
C12 A:E8V401 2.4 50.3 1.0
CB A:PHE48 2.6 61.0 1.0
O1 A:E8V401 2.6 48.1 1.0
NZ A:LYS71 2.7 40.0 1.0
CD1 A:ILE51 2.9 46.0 1.0
O A:HOH529 3.0 58.7 1.0
CE A:LYS71 3.1 42.0 1.0
CG A:PHE48 3.3 63.7 1.0
O A:PHE48 3.4 60.5 1.0
CD A:LYS71 3.5 40.1 1.0
C9 A:E8V401 3.6 49.7 1.0
C6 A:E8V401 3.6 43.7 1.0
CA A:PHE48 3.9 59.7 1.0
CD1 A:PHE48 3.9 65.1 1.0
C A:PHE48 4.1 58.2 1.0
CD2 A:PHE48 4.1 62.2 1.0
C8 A:E8V401 4.1 47.9 1.0
O A:HOH646 4.3 54.1 1.0
CG1 A:ILE51 4.3 40.3 1.0
CG A:LYS71 4.4 34.0 1.0
F1 A:E8V401 4.7 51.1 1.0
C1 A:E8V401 4.9 42.8 1.0
O A:HOH501 4.9 27.2 1.0

Fluorine binding site 3 out of 12 in 6bu6

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Fluorine binding site 3 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.2
occ:1.00
 F3 A:E8V401 0.0 69.2 1.0
C16 A:E8V401 1.4 74.2 1.0
C17 A:E8V401 2.4 70.4 1.0
C15 A:E8V401 2.4 77.2 1.0
O2 A:E8V401 2.8 90.2 1.0
C14 A:E8V401 3.6 74.7 1.0
C7 A:E8V401 3.6 63.8 1.0
C13 A:E8V401 4.1 70.0 1.0
CG1 A:ILE43 4.2 42.3 1.0
CD1 A:ILE43 4.4 43.7 1.0
CA A:GLY44 4.4 61.1 1.0
N A:GLY44 4.6 53.7 1.0
O A:GLY135 4.7 34.8 1.0
F4 A:E8V401 4.8 58.9 1.0
C4 A:E8V401 4.9 47.9 1.0

Fluorine binding site 4 out of 12 in 6bu6

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Fluorine binding site 4 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:58.9
occ:1.00
 F4 A:E8V401 0.0 58.9 1.0
C14 A:E8V401 1.4 74.7 1.0
C13 A:E8V401 2.4 70.0 1.0
C15 A:E8V401 2.4 77.2 1.0
O A:HOH766 2.5 69.1 1.0
O2 A:E8V401 2.8 90.2 1.0
C16 A:E8V401 3.6 74.2 1.0
C7 A:E8V401 3.7 63.8 1.0
N A:GLN45 3.7 73.1 1.0
CA A:GLY44 3.8 61.1 1.0
CE2 A:PHE48 4.1 62.6 1.0
C17 A:E8V401 4.1 70.4 1.0
C A:GLY44 4.2 68.9 1.0
CD2 A:PHE48 4.3 62.2 1.0
CA A:GLN45 4.7 72.9 1.0
F3 A:E8V401 4.8 69.2 1.0
O A:HOH648 4.8 42.3 1.0
OD2 A:ASP137 4.8 46.2 1.0
N A:GLY47 4.9 60.8 1.0
C4 A:E8V401 4.9 47.9 1.0
C A:GLN45 4.9 72.3 1.0
O A:HOH620 5.0 47.1 1.0
CB A:GLN45 5.0 71.6 1.0

Fluorine binding site 5 out of 12 in 6bu6

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Fluorine binding site 5 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:69.0
occ:1.00
 F1 B:E8V401 0.0 69.0 1.0
C9 B:E8V401 1.4 66.3 1.0
C8 B:E8V401 2.4 60.2 1.0
C10 B:E8V401 2.4 69.2 1.0
O1 B:E8V401 2.8 69.5 1.0
OD1 B:ASP137 3.5 56.4 1.0
C11 B:E8V401 3.6 69.7 1.0
C6 B:E8V401 3.6 56.4 1.0
CE B:LYS140 3.7 60.1 1.0
NZ B:LYS140 3.7 61.4 1.0
N B:ASP137 3.8 38.7 1.0
O B:GLY135 3.9 42.2 1.0
C12 B:E8V401 4.1 64.2 1.0
CA B:SER136 4.1 40.9 1.0
CD B:LYS140 4.3 57.4 1.0
C B:SER136 4.3 37.6 1.0
CG B:ASP137 4.4 47.0 1.0
CB B:ASP137 4.5 44.9 1.0
CA B:ASP137 4.7 40.3 1.0
F2 B:E8V401 4.8 75.7 1.0
C B:GLY135 4.8 40.0 1.0
C1 B:E8V401 4.9 50.3 1.0
OG B:SER136 4.9 47.4 1.0
N2 B:E8V401 4.9 51.1 1.0
N B:SER136 5.0 38.6 1.0

Fluorine binding site 6 out of 12 in 6bu6

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Fluorine binding site 6 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:75.7
occ:1.00
 F2 B:E8V401 0.0 75.7 1.0
C11 B:E8V401 1.4 69.7 1.0
C12 B:E8V401 2.4 64.2 1.0
C10 B:E8V401 2.4 69.2 1.0
O1 B:E8V401 2.8 69.5 1.0
CA B:GLY44 3.2 92.6 1.0
N B:GLN45 3.2 98.3 1.0
C B:GLY44 3.5 93.7 1.0
C6 B:E8V401 3.6 56.4 1.0
C9 B:E8V401 3.6 66.3 1.0
O B:ILE43 3.7 86.3 1.0
N B:GLY47 3.8 82.3 1.0
N B:GLY46 3.8 94.3 1.0
CD2 B:PHE48 4.0 62.7 1.0
CE2 B:PHE48 4.1 61.0 1.0
C8 B:E8V401 4.1 60.2 1.0
N B:GLY44 4.1 89.7 1.0
C B:GLN45 4.2 97.8 1.0
C B:ILE43 4.3 85.6 1.0
CA B:GLN45 4.3 98.7 1.0
O B:GLY44 4.4 85.1 1.0
CA B:GLY47 4.5 77.8 1.0
CA B:GLY46 4.6 88.8 1.0
C B:GLY46 4.6 87.4 1.0
F1 B:E8V401 4.8 69.0 1.0
N B:PHE48 4.8 72.0 1.0
C1 B:E8V401 4.8 50.3 1.0

Fluorine binding site 7 out of 12 in 6bu6

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Fluorine binding site 7 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:49.1
occ:1.00
 F3 B:E8V401 0.0 49.1 1.0
C16 B:E8V401 1.4 51.9 1.0
C17 B:E8V401 2.4 49.3 1.0
C15 B:E8V401 2.4 56.6 1.0
O2 B:E8V401 2.8 58.9 1.0
O B:HOH503 3.3 45.6 1.0
CB B:MET131 3.4 40.8 1.0
CG B:MET131 3.4 41.5 1.0
CE B:MET131 3.5 39.8 1.0
C14 B:E8V401 3.6 59.4 1.0
C7 B:E8V401 3.6 49.1 1.0
CB B:PRO111 3.9 29.9 1.0
CG B:PRO111 4.0 29.6 1.0
C13 B:E8V401 4.1 56.4 1.0
CE2 B:PHE134 4.2 37.8 1.0
SD B:MET131 4.2 41.2 1.0
OH B:TYR87 4.3 37.8 1.0
O B:ASP132 4.5 39.0 1.0
CG1 B:VAL196 4.6 31.8 1.0
CB B:VAL196 4.7 32.3 1.0
F4 B:E8V401 4.7 69.3 1.0
CD B:LYS71 4.8 71.9 1.0
CA B:MET131 4.8 41.4 1.0
C4 B:E8V401 4.9 48.6 1.0
CD2 B:PHE134 4.9 38.0 1.0

Fluorine binding site 8 out of 12 in 6bu6

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Fluorine binding site 8 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:69.3
occ:1.00
 F4 B:E8V401 0.0 69.3 1.0
C14 B:E8V401 1.4 59.4 1.0
C15 B:E8V401 2.4 56.6 1.0
C13 B:E8V401 2.4 56.4 1.0
O2 B:E8V401 2.7 58.9 1.0
NZ B:LYS71 2.9 71.8 1.0
CB B:PHE48 3.3 64.2 1.0
CG B:PHE48 3.4 63.4 1.0
O B:HOH547 3.5 52.0 1.0
CD1 B:PHE48 3.6 62.7 1.0
C16 B:E8V401 3.6 51.9 1.0
C7 B:E8V401 3.7 49.1 1.0
CE B:LYS71 3.7 72.5 1.0
CD B:LYS71 3.9 71.9 1.0
C17 B:E8V401 4.1 49.3 1.0
CD1 B:ILE51 4.1 74.2 1.0
CD2 B:PHE48 4.2 62.7 1.0
CG2 B:VAL196 4.3 32.0 1.0
N B:ASP197 4.4 31.8 1.0
CE1 B:PHE48 4.5 62.5 1.0
CB B:VAL196 4.5 32.3 1.0
CA B:ASP197 4.6 35.0 1.0
CB B:ASP197 4.6 38.0 1.0
O B:PHE48 4.7 67.6 1.0
CA B:PHE48 4.7 67.5 1.0
F3 B:E8V401 4.7 49.1 1.0
C4 B:E8V401 4.9 48.6 1.0
CE2 B:PHE48 4.9 61.0 1.0
O B:HOH503 4.9 45.6 1.0
CG B:LYS71 5.0 66.5 1.0

Fluorine binding site 9 out of 12 in 6bu6

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Fluorine binding site 9 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:41.8
occ:1.00
 F1 D:E8V401 0.0 41.8 1.0
C9 D:E8V401 1.4 40.5 1.0
C8 D:E8V401 2.4 36.5 1.0
C10 D:E8V401 2.4 41.0 1.0
O1 D:E8V401 2.7 37.8 1.0
O D:ILE43 3.2 65.2 1.0
CA D:GLY44 3.3 71.9 1.0
O D:GLY44 3.5 75.1 1.0
C D:GLY44 3.6 76.2 1.0
C11 D:E8V401 3.6 40.5 1.0
C6 D:E8V401 3.6 34.9 1.0
C D:ILE43 3.6 73.2 1.0
N D:GLY44 3.7 74.2 1.0
N D:GLY47 3.9 78.7 1.0
C12 D:E8V401 4.1 37.3 1.0
CD2 D:PHE48 4.1 60.7 1.0
CE2 D:PHE48 4.3 60.8 1.0
CA D:GLY47 4.6 81.4 1.0
F2 D:E8V401 4.8 43.0 1.0
CB D:ILE43 4.8 72.4 1.0
CA D:ILE43 4.8 68.1 1.0
C1 D:E8V401 4.8 33.3 1.0
N D:PHE48 4.9 77.9 1.0

Fluorine binding site 10 out of 12 in 6bu6

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Fluorine binding site 10 out of 12 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis- Difluorophenol-Aminopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:43.0
occ:1.00
 F2 D:E8V401 0.0 43.0 1.0
C11 D:E8V401 1.4 40.5 1.0
C12 D:E8V401 2.4 37.3 1.0
C10 D:E8V401 2.4 41.0 1.0
O1 D:E8V401 2.8 37.8 1.0
CE D:LYS140 3.3 45.6 1.0
OD1 D:ASP137 3.3 45.5 1.0
NZ D:LYS140 3.4 46.6 1.0
C9 D:E8V401 3.6 40.5 1.0
C6 D:E8V401 3.6 34.9 1.0
N D:ASP137 3.7 31.5 1.0
CA D:SER136 4.1 33.9 1.0
O D:GLY135 4.1 36.4 1.0
C8 D:E8V401 4.1 36.5 1.0
CG D:ASP137 4.3 40.6 1.0
C D:SER136 4.3 31.0 1.0
CD D:LYS140 4.4 45.5 1.0
CB D:ASP137 4.5 35.8 1.0
OG D:SER136 4.7 35.5 1.0
CA D:ASP137 4.7 33.6 1.0
F1 D:E8V401 4.8 41.8 1.0
C1 D:E8V401 4.9 33.3 1.0
C D:GLY135 4.9 35.7 1.0
N D:SER136 5.0 34.8 1.0
CB D:SER136 5.0 36.6 1.0

Reference:

R.M.Counago, C.V.Dos Reis, G.P.De Souza, A.S.Santiago, H.Azevedo, C.Guimaraes, A.Mascarello, F.Gama, M.Ferreira, K.B.Massirer, P.Arruda, A.M.Edwards, J.M.Elkins, Structural Genomics Consortium (Sgc). Crystal Structure of the Human Vaccinia-Related Kinase Bound to A Bis-Difluorophenol-Aminopyridine Inhibitor To Be Published.
Page generated: Thu Aug 1 18:22:05 2024

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