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Fluorine in PDB 6cnx: Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor

Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor

All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor, PDB code: 6cnx was solved by R.M.Counago, C.V.Dos Reis, G.P.De Souza, 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) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.470, 96.821, 192.831, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.1

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 8 in 6cnx

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Fluorine binding site 1 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.5
occ:1.00
 F1 A:F87401 0.0 34.5 1.0
C20 A:F87401 1.3 33.5 1.0
C21 A:F87401 2.3 32.5 1.0
C19 A:F87401 2.4 32.5 1.0
O2 A:F87401 2.7 30.4 1.0
O A:HOH502 3.3 24.1 1.0
OH A:TYR87 3.4 26.4 1.0
CB A:PRO111 3.5 20.9 1.0
CE A:MET131 3.5 29.6 1.0
C18 A:F87401 3.6 33.5 1.0
C16 A:F87401 3.6 31.5 1.0
CG A:PRO111 3.8 20.5 1.0
CB A:MET131 3.9 26.1 1.0
CG A:MET131 4.0 27.3 1.0
C17 A:F87401 4.1 32.2 1.0
CG1 A:VAL196 4.2 22.3 1.0
CE2 A:PHE134 4.2 26.2 1.0
CZ A:TYR87 4.2 26.9 1.0
CB A:VAL196 4.4 21.9 1.0
SD A:MET131 4.5 30.0 1.0
F2 A:F87401 4.7 36.1 1.0
CE2 A:TYR87 4.7 26.8 1.0
N5 A:F87401 4.7 31.4 1.0
O A:ASP132 4.8 24.1 1.0
CD2 A:PHE134 4.9 25.7 1.0
CA A:PRO111 5.0 21.6 1.0

Fluorine binding site 2 out of 8 in 6cnx

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Fluorine binding site 2 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.1
occ:1.00
 F2 A:F87401 0.0 36.1 1.0
C18 A:F87401 1.3 33.5 1.0
C19 A:F87401 2.3 32.5 1.0
C17 A:F87401 2.3 32.2 1.0
O2 A:F87401 2.7 30.4 1.0
NZ A:LYS71 2.9 30.8 1.0
O A:HOH527 3.4 34.8 1.0
C12 A:F87401 3.4 38.4 1.0
CD1 A:ILE51 3.5 28.0 1.0
C14 A:F87401 3.6 38.5 1.0
CD A:LYS71 3.6 28.6 1.0
C20 A:F87401 3.6 33.5 1.0
C16 A:F87401 3.6 31.5 1.0
CE A:LYS71 3.8 29.6 1.0
CG A:LYS71 3.9 27.6 1.0
O A:HOH547 4.0 47.0 1.0
O A:HOH704 4.0 59.9 1.0
C21 A:F87401 4.1 32.5 1.0
C13 A:F87401 4.2 39.0 1.0
C11 A:F87401 4.5 37.0 1.0
CG1 A:ILE51 4.5 28.1 1.0
F1 A:F87401 4.7 34.5 1.0
N5 A:F87401 4.8 31.4 1.0
N1 A:F87401 4.8 32.1 1.0
C10 A:F87401 4.8 36.6 1.0
O A:HOH502 4.9 24.1 1.0

Fluorine binding site 3 out of 8 in 6cnx

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Fluorine binding site 3 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:34.0
occ:1.00
 F1 B:F87401 0.0 34.0 1.0
C20 B:F87401 1.3 36.1 1.0
C21 B:F87401 2.3 37.5 1.0
C19 B:F87401 2.3 36.4 1.0
O2 B:F87401 2.7 35.2 1.0
O B:HOH501 3.2 29.1 1.0
CE B:MET131 3.4 29.0 1.0
CB B:MET131 3.4 32.4 1.0
CG B:MET131 3.5 31.9 1.0
CB B:PRO111 3.6 27.2 1.0
C18 B:F87401 3.6 37.9 1.0
C16 B:F87401 3.6 38.4 1.0
CG B:PRO111 3.8 26.0 1.0
OH B:TYR87 3.9 28.7 1.0
C17 B:F87401 4.1 38.5 1.0
SD B:MET131 4.3 30.7 1.0
CE2 B:PHE134 4.4 31.1 1.0
CG1 B:VAL196 4.5 28.4 1.0
CB B:VAL196 4.6 28.2 1.0
O B:ASP132 4.7 32.9 1.0
F2 B:F87401 4.7 39.9 1.0
N5 B:F87401 4.8 39.7 1.0
CZ B:TYR87 4.8 29.2 1.0
CA B:MET131 4.9 33.9 1.0
NZ B:LYS71 5.0 38.1 1.0

Fluorine binding site 4 out of 8 in 6cnx

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Fluorine binding site 4 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:39.9
occ:1.00
 F2 B:F87401 0.0 39.9 1.0
C18 B:F87401 1.3 37.9 1.0
C17 B:F87401 2.3 38.5 1.0
C19 B:F87401 2.4 36.4 1.0
O2 B:F87401 2.7 35.2 1.0
C12 B:F87401 3.2 43.0 1.0
NZ B:LYS71 3.4 38.1 1.0
C20 B:F87401 3.6 36.1 1.0
C16 B:F87401 3.6 38.4 1.0
C14 B:F87401 3.7 41.1 1.0
O B:HOH612 3.9 41.9 1.0
C11 B:F87401 3.9 42.9 1.0
CG2 B:VAL196 3.9 28.6 1.0
CD1 B:ILE51 4.1 48.6 1.0
CE B:LYS71 4.1 40.1 1.0
C21 B:F87401 4.1 37.5 1.0
C13 B:F87401 4.1 44.5 1.0
CB B:VAL196 4.2 28.2 1.0
C10 B:F87401 4.4 44.1 1.0
CD B:LYS71 4.5 40.4 1.0
N1 B:F87401 4.6 40.7 1.0
N B:ASP197 4.6 28.1 1.0
F1 B:F87401 4.7 34.0 1.0
N5 B:F87401 4.8 39.7 1.0
CG1 B:VAL196 5.0 28.4 1.0

Fluorine binding site 5 out of 8 in 6cnx

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Fluorine binding site 5 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:38.5
occ:1.00
 F1 C:FCS401 0.0 38.5 1.0
C20 C:FCS401 1.3 42.0 1.0
C21 C:FCS401 2.3 43.3 1.0
C19 C:FCS401 2.3 43.1 1.0
O2 C:FCS401 2.8 44.6 1.0
OH C:TYR87 3.2 23.4 1.0
CB C:MET131 3.2 27.9 1.0
CG C:MET131 3.4 30.2 1.0
CE C:MET131 3.5 35.0 1.0
CB C:PRO111 3.5 21.7 1.0
C18 C:FCS401 3.6 44.0 1.0
C16 C:FCS401 3.6 42.7 1.0
CZ C:TYR87 3.7 23.4 1.0
CG C:PRO111 3.9 21.1 1.0
CE2 C:TYR87 4.1 23.2 1.0
C17 C:FCS401 4.1 44.6 1.0
SD C:MET131 4.2 33.9 1.0
CE1 C:TYR87 4.5 24.2 1.0
O C:ASP132 4.5 26.0 1.0
CE2 C:PHE134 4.6 23.6 1.0
CA C:MET131 4.7 26.8 1.0
F2 C:FCS401 4.7 47.2 1.0
N5 C:FCS401 4.7 41.5 1.0
N C:ASP132 4.8 25.2 1.0
CG1 C:VAL196 5.0 22.6 1.0
CA C:PRO111 5.0 21.3 1.0

Fluorine binding site 6 out of 8 in 6cnx

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Fluorine binding site 6 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:47.2
occ:1.00
 F2 C:FCS401 0.0 47.2 1.0
C18 C:FCS401 1.3 44.0 1.0
C19 C:FCS401 2.3 43.1 1.0
C17 C:FCS401 2.3 44.6 1.0
O2 C:FCS401 2.7 44.6 1.0
O C:HOH707 2.9 43.8 1.0
NZ C:LYS71 3.2 36.9 1.0
C20 C:FCS401 3.6 42.0 1.0
C16 C:FCS401 3.6 42.7 1.0
C12 C:FCS401 3.7 46.8 1.0
CB C:VAL196 4.1 22.2 1.0
C21 C:FCS401 4.1 43.3 1.0
CG2 C:VAL196 4.1 22.8 1.0
C13 C:FCS401 4.3 47.6 1.0
CE C:LYS71 4.3 36.6 1.0
N C:ASP197 4.4 22.6 1.0
C14 C:FCS401 4.5 46.1 1.0
C11 C:FCS401 4.6 47.0 1.0
CD C:LYS71 4.6 36.0 1.0
F1 C:FCS401 4.7 38.5 1.0
C10 C:FCS401 4.7 46.9 1.0
N1 C:FCS401 4.7 41.8 1.0
CG1 C:VAL196 4.8 22.6 1.0
N5 C:FCS401 4.8 41.5 1.0
CA C:ASP197 4.8 24.0 1.0
OE2 C:GLU83 4.9 22.0 1.0

Fluorine binding site 7 out of 8 in 6cnx

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Fluorine binding site 7 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:27.8
occ:1.00
 F1 D:F87401 0.0 27.8 1.0
C20 D:F87401 1.3 29.6 1.0
C21 D:F87401 2.3 30.5 1.0
C19 D:F87401 2.3 30.2 1.0
O2 D:F87401 2.7 28.9 1.0
O D:HOH511 3.3 23.3 1.0
CE D:MET131 3.4 24.6 1.0
CB D:MET131 3.5 27.6 1.0
CG D:MET131 3.6 27.3 1.0
C18 D:F87401 3.6 32.0 1.0
C16 D:F87401 3.6 32.1 1.0
CB D:PRO111 3.6 23.3 1.0
CG D:PRO111 3.7 22.4 1.0
OH D:TYR87 4.0 23.2 1.0
C17 D:F87401 4.1 32.2 1.0
CG1 D:VAL196 4.2 23.6 1.0
SD D:MET131 4.3 26.3 1.0
CB D:VAL196 4.3 23.3 1.0
CE2 D:PHE134 4.4 26.9 1.0
F2 D:F87401 4.7 34.8 1.0
O D:ASP132 4.7 29.3 1.0
N5 D:F87401 4.7 33.3 1.0
CZ D:TYR87 4.9 24.1 1.0
CA D:MET131 4.9 29.0 1.0
CD D:LYS71 5.0 35.5 1.0
NZ D:LYS71 5.0 33.1 1.0

Fluorine binding site 8 out of 8 in 6cnx

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Fluorine binding site 8 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin 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 1 (VRK1) Bound to An N-Propynyl-N-Isopentyl-Dihydropteridin Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:34.8
occ:1.00
 F2 D:F87401 0.0 34.8 1.0
C18 D:F87401 1.3 32.0 1.0
C17 D:F87401 2.3 32.2 1.0
C19 D:F87401 2.4 30.2 1.0
O2 D:F87401 2.7 28.9 1.0
C12 D:F87401 3.3 36.0 1.0
NZ D:LYS71 3.3 33.1 1.0
C14 D:F87401 3.4 34.8 1.0
O D:HOH663 3.5 45.7 1.0
C20 D:F87401 3.6 29.6 1.0
C16 D:F87401 3.6 32.1 1.0
CD1 D:ILE51 3.9 46.0 1.0
CE D:LYS71 3.9 34.9 1.0
C11 D:F87401 4.0 36.0 1.0
CD D:LYS71 4.1 35.5 1.0
C21 D:F87401 4.1 30.5 1.0
CG2 D:VAL196 4.1 23.7 1.0
CB D:VAL196 4.4 23.3 1.0
C13 D:F87401 4.5 38.0 1.0
C10 D:F87401 4.6 36.9 1.0
F1 D:F87401 4.7 27.8 1.0
N1 D:F87401 4.7 34.2 1.0
CG D:LYS71 4.7 36.8 1.0
N D:ASP197 4.8 24.0 1.0
N5 D:F87401 4.8 33.3 1.0

Reference:

R.M.Counago, C.V.Dos Reis, G.P.De Souza, F.Gama, H.Azevedo, C.Guimaraes, A.Mascarello, 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 1 (VRK1) Bound to A N-Propynyl-N-Isopentil-Dihydropteridine Inhibitor To Be Published.
Page generated: Thu Aug 1 18:35:21 2024

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