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Fluorine in PDB 6ncg: Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor

Enzymatic activity of Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor

All present enzymatic activity of Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor, PDB code: 6ncg was solved by C.V.Dos Reis, C.G.Chiodi, G.P.De Souza, C.Guimaraes, A.Mascarello, F.Gama, M.Ferreira, R.M.Counago, K.B.Massirer, J.M.Elkins, P.Arruda, A.M.Edwards, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.528, 67.625, 171.346, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 29.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor (pdb code 6ncg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor, PDB code: 6ncg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ncg

Go back to Fluorine Binding Sites List in 6ncg
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide 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 Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:82.9
occ:1.00
 F1 A:KJD401 0.0 82.9 1.0
C9 A:KJD401 1.4 76.5 1.0
C8 A:KJD401 2.4 72.9 1.0
C10 A:KJD401 2.4 85.1 1.0
O1 A:KJD401 2.7 83.6 1.0
N A:ASP186 3.0 52.0 1.0
OH A:TYR77 3.3 70.0 1.0
CB A:ALA185 3.4 50.9 1.0
C11 A:KJD401 3.6 92.3 1.0
C6 A:KJD401 3.6 70.2 1.0
CA A:ASP186 3.8 49.7 1.0
CA A:ALA185 3.9 51.0 1.0
C A:ALA185 3.9 49.6 1.0
SD A:MET121 3.9 79.8 1.0
CE A:MET121 4.1 77.7 1.0
C12 A:KJD401 4.1 81.2 1.0
OE2 A:GLU73 4.3 69.9 1.0
CZ A:TYR77 4.6 60.6 1.0
CB A:ASP186 4.6 50.1 1.0
F2 A:KJD401 4.7 0.0 1.0
N2 A:KJD401 4.8 70.8 1.0
CG A:PRO101 4.8 57.3 1.0
C1 A:KJD401 4.9 65.9 1.0
C A:ASP186 5.0 49.2 1.0
N A:TYR187 5.0 50.1 1.0

Fluorine binding site 2 out of 4 in 6ncg

Go back to Fluorine Binding Sites List in 6ncg
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide 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 Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:0.0
occ:1.00
 F2 A:KJD401 0.0 0.0 1.0
C11 A:KJD401 1.4 92.3 1.0
C12 A:KJD401 2.4 81.2 1.0
C10 A:KJD401 2.4 85.1 1.0
CD1 A:ILE43 2.7 95.2 1.0
O1 A:KJD401 2.8 83.6 1.0
C9 A:KJD401 3.6 76.5 1.0
C6 A:KJD401 3.6 70.2 1.0
CG1 A:ILE43 3.6 89.2 1.0
C8 A:KJD401 4.1 72.9 1.0
CB A:LYS61 4.6 61.5 1.0
F1 A:KJD401 4.7 82.9 1.0
CG2 A:ILE43 4.8 83.2 1.0
CE A:MET121 4.8 77.7 1.0
CB A:ILE43 4.8 84.6 1.0
C1 A:KJD401 4.9 65.9 1.0

Fluorine binding site 3 out of 4 in 6ncg

Go back to Fluorine Binding Sites List in 6ncg
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide 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 Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:76.1
occ:1.00
 F1 B:KJD600 0.0 76.1 1.0
C9 B:KJD600 1.4 73.2 1.0
C8 B:KJD600 2.4 75.8 1.0
C10 B:KJD600 2.4 70.7 1.0
O1 B:KJD600 2.7 72.8 1.0
OH B:TYR77 2.9 57.3 1.0
CB B:ALA185 3.2 54.8 1.0
C11 B:KJD600 3.6 74.8 1.0
C6 B:KJD600 3.6 73.3 1.0
CG B:PRO101 3.8 53.9 1.0
SD B:MET121 3.9 89.9 1.0
CA B:ALA185 3.9 54.6 1.0
N B:ASP186 4.1 63.5 1.0
C12 B:KJD600 4.1 71.3 1.0
CZ B:TYR77 4.1 49.5 1.0
C B:ALA185 4.6 57.9 1.0
N2 B:KJD600 4.7 65.6 1.0
F2 B:KJD600 4.7 85.3 1.0
CB B:PRO101 4.7 53.5 1.0
CE B:MET121 4.7 89.3 1.0
OE2 B:GLU73 4.8 73.7 1.0
CD B:PRO101 4.8 51.9 1.0
C1 B:KJD600 4.9 72.8 1.0
CE2 B:TYR77 4.9 47.4 1.0
CE1 B:TYR77 4.9 49.7 1.0

Fluorine binding site 4 out of 4 in 6ncg

Go back to Fluorine Binding Sites List in 6ncg
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide 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 Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:85.3
occ:1.00
 F2 B:KJD600 0.0 85.3 1.0
C11 B:KJD600 1.4 74.8 1.0
C12 B:KJD600 2.4 71.3 1.0
C10 B:KJD600 2.4 70.7 1.0
NZ B:LYS61 2.6 93.2 1.0
O1 B:KJD600 2.7 72.8 1.0
CE B:LYS61 3.2 87.7 1.0
CD B:LYS61 3.5 80.4 1.0
C9 B:KJD600 3.6 73.2 1.0
CD1 B:ILE43 3.6 80.1 1.0
C6 B:KJD600 3.6 73.3 1.0
C8 B:KJD600 4.1 75.8 1.0
CG1 B:ILE43 4.2 81.3 1.0
CG B:LYS61 4.6 74.8 1.0
F1 B:KJD600 4.7 76.1 1.0
C1 B:KJD600 4.9 72.8 1.0

Reference:

C.V.Dos Reis, C.G.Chiodi, G.P.De Souza, H.Azevedo, C.Guimaraes, A.Mascarello, F.Gama, M.Ferreira, R.M.Counago, K.B.Massirer, P.Arruda, J.M.Elkins, A.M.Edwards, Structural Genomics Consortium (Sgc). Crystal Structure of Human Vaccinia-Related Kinase 2 (Vrk-2) Bound to Pyridin-Benzenesulfonamide Inhibitor To Be Published.
Page generated: Tue Jul 15 13:19:07 2025

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