Fluorine in PDB 6vxu: Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471

Enzymatic activity of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471

All present enzymatic activity of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471:
2.7.11.1;

Protein crystallography data

The structure of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471, PDB code: 6vxu was solved by C.V.Dos Reis, L.A.Dutra, F.H.Gama, A.Mascarello, H.Azevedo, C.R.Guimaraes, K.B.Massirer, P.Arruda, A.M.Edwards, R.M.Counago, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.771, 96.3, 191.988, 90, 90, 90
R / Rfree (%) 18.4 / 20.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 (pdb code 6vxu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471, PDB code: 6vxu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6vxu

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Fluorine binding site 1 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.0
occ:1.00
 F1 A:RTJ401 0.0 44.0 1.0
C6 A:RTJ401 1.3 45.8 1.0
C1 A:RTJ401 2.3 46.2 1.0
C5 A:RTJ401 2.4 44.9 1.0
O2 A:RTJ401 2.7 42.5 1.0
CB A:MET131 3.2 33.1 1.0
CB A:PRO111 3.3 30.1 1.0
CE A:MET131 3.3 37.7 1.0
OH A:TYR87 3.3 34.3 1.0
CG A:MET131 3.4 35.1 1.0
C4 A:RTJ401 3.6 49.8 1.0
C2 A:RTJ401 3.6 48.7 1.0
CG A:PRO111 3.7 29.8 1.0
CZ A:TYR87 3.8 33.7 1.0
CE2 A:TYR87 4.1 33.6 1.0
C3 A:RTJ401 4.1 49.1 1.0
SD A:MET131 4.1 38.3 1.0
CE2 A:PHE134 4.3 32.7 1.0
CE1 A:TYR87 4.6 34.1 1.0
CA A:MET131 4.6 30.6 1.0
F2 A:RTJ401 4.7 39.2 1.0
O A:ASP132 4.7 31.1 1.0
CA A:PRO111 4.7 31.1 1.0
N A:ASP132 4.7 30.8 1.0
N1 A:RTJ401 4.8 44.8 1.0
CG1 A:VAL196 4.8 33.2 1.0

Fluorine binding site 2 out of 8 in 6vxu

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Fluorine binding site 2 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.2
occ:1.00
 F2 A:RTJ401 0.0 39.2 1.0
C4 A:RTJ401 1.3 49.8 1.0
C3 A:RTJ401 2.3 49.1 1.0
C5 A:RTJ401 2.3 44.9 1.0
O A:HOH501 2.6 50.2 1.0
O2 A:RTJ401 2.7 42.5 1.0
NZ A:LYS71 3.4 45.4 1.0
C20 A:RTJ401 3.5 44.8 1.0
C6 A:RTJ401 3.6 45.8 1.0
C2 A:RTJ401 3.6 48.7 1.0
CD A:LYS71 3.9 41.5 1.0
C18 A:RTJ401 4.0 44.7 1.0
CE A:LYS71 4.1 43.5 1.0
C1 A:RTJ401 4.1 46.2 1.0
CD1 A:ILE51 4.4 37.1 1.0
CB A:VAL196 4.4 32.6 1.0
CG2 A:VAL196 4.6 32.7 1.0
N3 A:RTJ401 4.7 43.6 1.0
C17 A:RTJ401 4.7 41.8 1.0
F1 A:RTJ401 4.7 44.0 1.0
N1 A:RTJ401 4.8 44.8 1.0
N A:ASP197 4.8 33.6 1.0
C19 A:RTJ401 4.9 46.0 1.0
CG A:LYS71 5.0 39.7 1.0
CG1 A:VAL196 5.0 33.2 1.0
OE2 A:GLU83 5.0 34.2 1.0

Fluorine binding site 3 out of 8 in 6vxu

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Fluorine binding site 3 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.5
occ:1.00
 F1 B:RTJ401 0.0 52.5 1.0
C6 B:RTJ401 1.3 59.8 1.0
C1 B:RTJ401 2.3 59.3 1.0
C5 B:RTJ401 2.3 60.3 1.0
O2 B:RTJ401 2.7 45.4 1.0
NZ B:LYS71 3.4 53.1 1.0
C4 B:RTJ401 3.6 67.4 1.0
C2 B:RTJ401 3.6 62.8 1.0
CD1 B:ILE51 3.6 66.0 1.0
CE B:LYS71 3.7 55.2 1.0
C19 B:RTJ401 4.1 59.4 1.0
C3 B:RTJ401 4.1 65.3 1.0
CD B:LYS71 4.2 55.4 1.0
C20 B:RTJ401 4.2 58.6 1.0
CG2 B:VAL196 4.3 40.6 1.0
CB B:VAL196 4.4 40.7 1.0
C17 B:RTJ401 4.5 56.1 1.0
N B:ASP197 4.6 41.3 1.0
N3 B:RTJ401 4.6 56.3 1.0
F2 B:RTJ401 4.7 45.7 1.0
C18 B:RTJ401 4.7 59.5 1.0
N1 B:RTJ401 4.8 59.9 1.0
CG B:LYS71 4.9 57.3 1.0
CG1 B:ILE51 4.9 67.4 1.0
CA B:ASP197 4.9 42.9 1.0
CB B:ASP197 5.0 44.6 1.0

Fluorine binding site 4 out of 8 in 6vxu

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Fluorine binding site 4 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.7
occ:1.00
 F2 B:RTJ401 0.0 45.7 1.0
C4 B:RTJ401 1.4 67.4 1.0
C3 B:RTJ401 2.4 65.3 1.0
C5 B:RTJ401 2.4 60.3 1.0
O2 B:RTJ401 2.7 45.4 1.0
O B:HOH501 3.3 43.7 1.0
CB B:MET131 3.3 47.2 1.0
CG B:MET131 3.5 47.1 1.0
CE B:MET131 3.6 44.3 1.0
C6 B:RTJ401 3.6 59.8 1.0
C2 B:RTJ401 3.6 62.8 1.0
CB B:PRO111 3.7 40.4 1.0
CG B:PRO111 3.8 38.8 1.0
OH B:TYR87 4.1 40.7 1.0
C1 B:RTJ401 4.1 59.3 1.0
CE2 B:PHE134 4.3 42.9 1.0
SD B:MET131 4.3 47.1 1.0
CG1 B:VAL196 4.5 41.1 1.0
O B:ASP132 4.5 48.4 1.0
CB B:VAL196 4.5 40.7 1.0
F1 B:RTJ401 4.7 52.5 1.0
N1 B:RTJ401 4.8 59.9 1.0
CA B:MET131 4.8 48.8 1.0
N B:ASP132 4.9 47.7 1.0
CD B:LYS71 4.9 55.4 1.0
CZ B:TYR87 5.0 40.9 1.0

Fluorine binding site 5 out of 8 in 6vxu

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Fluorine binding site 5 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:58.1
occ:1.00
 F1 C:VBD401 0.0 58.1 1.0
C6 C:VBD401 1.4 61.4 1.0
C1 C:VBD401 2.3 61.9 1.0
C5 C:VBD401 2.4 62.0 1.0
O2 C:VBD401 2.7 56.1 1.0
OH C:TYR87 3.0 38.5 1.0
CB C:MET131 3.3 39.6 1.0
CE C:MET131 3.4 49.2 1.0
CG C:MET131 3.4 43.3 1.0
CZ C:TYR87 3.5 37.3 1.0
CB C:PRO111 3.5 31.5 1.0
C4 C:VBD401 3.6 65.9 1.0
C2 C:VBD401 3.6 64.7 1.0
CE2 C:TYR87 3.9 35.5 1.0
CG C:PRO111 3.9 31.0 1.0
SD C:MET131 4.1 48.4 1.0
C3 C:VBD401 4.1 64.7 1.0
CE1 C:TYR87 4.2 37.0 1.0
O C:ASP132 4.5 36.1 1.0
CE2 C:PHE134 4.6 36.4 1.0
CA C:MET131 4.7 37.0 1.0
F2 C:VBD401 4.7 52.3 1.0
N1 C:VBD401 4.8 62.5 1.0
N C:ASP132 4.9 34.6 1.0
CD2 C:TYR87 4.9 35.0 1.0
CG1 C:VAL196 4.9 33.8 1.0
CA C:PRO111 5.0 31.2 1.0

Fluorine binding site 6 out of 8 in 6vxu

Go back to Fluorine Binding Sites List in 6vxu
Fluorine binding site 6 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:52.3
occ:1.00
 F2 C:VBD401 0.0 52.3 1.0
C4 C:VBD401 1.3 65.9 1.0
C3 C:VBD401 2.3 64.7 1.0
C5 C:VBD401 2.4 62.0 1.0
O2 C:VBD401 2.7 56.1 1.0
C20 C:VBD401 3.1 60.8 1.0
NZ C:LYS71 3.2 45.0 1.0
C6 C:VBD401 3.6 61.4 1.0
C2 C:VBD401 3.6 64.7 1.0
C18 C:VBD401 3.7 59.1 1.0
CB C:VAL196 4.1 33.2 1.0
C1 C:VBD401 4.1 61.9 1.0
CE C:LYS71 4.2 44.3 1.0
CG2 C:VAL196 4.2 33.7 1.0
CD C:LYS71 4.3 44.0 1.0
C19 C:VBD401 4.4 61.7 1.0
N C:ASP197 4.5 34.4 1.0
C17 C:VBD401 4.6 56.5 1.0
N3 C:VBD401 4.6 57.5 1.0
CG1 C:VAL196 4.7 33.8 1.0
F1 C:VBD401 4.7 58.1 1.0
N1 C:VBD401 4.8 62.5 1.0
OE2 C:GLU83 4.8 36.4 1.0
CA C:ASP197 4.9 35.4 1.0

Fluorine binding site 7 out of 8 in 6vxu

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Fluorine binding site 7 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:44.4
occ:1.00
 F1 D:RTJ401 0.0 44.4 1.0
C6 D:RTJ401 1.3 50.8 1.0
C1 D:RTJ401 2.3 51.8 1.0
C5 D:RTJ401 2.3 49.6 1.0
O2 D:RTJ401 2.7 38.6 1.0
C20 D:RTJ401 3.2 45.2 1.0
NZ D:LYS71 3.2 43.1 1.0
CE D:LYS71 3.6 44.6 1.0
C4 D:RTJ401 3.6 51.0 1.0
C2 D:RTJ401 3.6 48.6 1.0
C18 D:RTJ401 3.6 45.3 1.0
CD1 D:ILE51 3.8 56.9 1.0
CD D:LYS71 4.0 44.8 1.0
CG2 D:VAL196 4.0 33.5 1.0
C3 D:RTJ401 4.1 50.0 1.0
O D:HOH534 4.1 56.2 1.0
CB D:VAL196 4.3 33.0 1.0
C19 D:RTJ401 4.3 45.9 1.0
N3 D:RTJ401 4.6 43.5 1.0
C17 D:RTJ401 4.6 42.9 1.0
F2 D:RTJ401 4.7 37.1 1.0
CG D:LYS71 4.7 45.9 1.0
N1 D:RTJ401 4.7 47.7 1.0
N D:ASP197 4.8 32.9 1.0

Fluorine binding site 8 out of 8 in 6vxu

Go back to Fluorine Binding Sites List in 6vxu
Fluorine binding site 8 out of 8 in the Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:37.1
occ:1.00
 F2 D:RTJ401 0.0 37.1 1.0
C4 D:RTJ401 1.3 51.0 1.0
C3 D:RTJ401 2.3 50.0 1.0
C5 D:RTJ401 2.3 49.6 1.0
O2 D:RTJ401 2.7 38.6 1.0
O D:HOH514 3.3 38.0 1.0
CE D:MET131 3.4 33.6 1.0
CB D:MET131 3.4 36.1 1.0
CG D:PRO111 3.6 30.2 1.0
C6 D:RTJ401 3.6 50.8 1.0
C2 D:RTJ401 3.6 48.6 1.0
CG D:MET131 3.6 36.0 1.0
CB D:PRO111 3.6 31.6 1.0
OH D:TYR87 3.9 31.7 1.0
C1 D:RTJ401 4.1 51.8 1.0
CG1 D:VAL196 4.2 33.6 1.0
CE2 D:PHE134 4.2 36.0 1.0
SD D:MET131 4.3 35.2 1.0
CB D:VAL196 4.4 33.0 1.0
O D:ASP132 4.7 37.9 1.0
F1 D:RTJ401 4.7 44.4 1.0
N1 D:RTJ401 4.7 47.7 1.0
CZ D:TYR87 4.8 31.9 1.0
CA D:MET131 4.9 37.3 1.0
CD D:PRO111 4.9 29.5 1.0
CD D:LYS71 4.9 44.8 1.0

Reference:

C.R.Guimaraes, R.M.Counago. Structure of Human Vaccinia-Related Kinase 1 (VRK1) Bound to ACH471 To Be Published.
Page generated: Sat Apr 3 15:03:17 2021

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