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Fluorine in PDB 4kbk: CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor

Enzymatic activity of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor

All present enzymatic activity of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor:
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor, PDB code: 4kbk was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.21 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.103, 84.760, 89.447, 108.06, 105.85, 93.09
R / Rfree (%) 19.1 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor (pdb code 4kbk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor, PDB code: 4kbk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4kbk

Go back to Fluorine Binding Sites List in 4kbk
Fluorine binding site 1 out of 4 in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.7
occ:1.00
 F1 A:1QG401 0.0 54.7 1.0
C8 A:1QG401 1.3 52.3 1.0
C7 A:1QG401 2.3 50.0 1.0
C9 A:1QG401 2.4 50.1 1.0
H8 A:1QG401 2.6 50.5 0.0
H7 A:1QG401 2.6 50.0 0.0
CE A:MET80 3.4 42.1 1.0
CB A:MET82 3.4 33.4 1.0
C6 A:1QG401 3.6 49.7 1.0
C10 A:1QG401 3.6 50.1 1.0
O A:MET80 3.6 34.7 1.0
CB A:LYS38 3.6 36.0 1.0
CG A:MET80 3.9 41.8 1.0
CE A:MET82 4.0 40.5 1.0
CB A:MET80 4.0 38.0 1.0
C A:MET80 4.1 37.5 1.0
N A:LYS38 4.1 35.6 1.0
C5 A:1QG401 4.1 48.9 1.0
N A:MET82 4.1 31.3 1.0
O A:ALA36 4.3 32.2 1.0
CG A:MET82 4.4 37.9 1.0
CA A:MET82 4.4 31.0 1.0
SD A:MET80 4.4 46.7 1.0
SD A:MET82 4.4 43.8 1.0
CD1 A:ILE68 4.5 42.0 1.0
CA A:LYS38 4.5 34.9 1.0
H6 A:1QG401 4.5 49.3 0.0
H9 A:1QG401 4.5 50.1 0.0
C A:VAL81 4.6 35.5 1.0
CD A:LYS38 4.6 41.9 1.0
N A:VAL81 4.7 33.9 1.0
CA A:MET80 4.7 36.0 1.0
CG A:LYS38 4.8 44.1 1.0
C A:ILE37 4.8 39.0 1.0
CA A:VAL81 4.9 33.4 1.0
C A:ALA36 5.0 33.4 1.0

Fluorine binding site 2 out of 4 in 4kbk

Go back to Fluorine Binding Sites List in 4kbk
Fluorine binding site 2 out of 4 in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:39.9
occ:1.00
 F1 B:1QG401 0.0 39.9 1.0
C8 B:1QG401 1.3 41.6 1.0
C7 B:1QG401 2.4 41.3 1.0
C9 B:1QG401 2.4 37.7 1.0
H7 B:1QG401 2.6 42.0 0.0
H8 B:1QG401 2.6 37.6 0.0
O B:MET80 3.3 31.3 1.0
CE B:MET80 3.4 39.7 1.0
CB B:LYS38 3.4 31.2 1.0
C6 B:1QG401 3.6 37.5 1.0
C10 B:1QG401 3.6 36.0 1.0
CB B:MET82 3.6 34.6 1.0
N B:LYS38 3.8 31.3 1.0
C B:MET80 3.8 34.0 1.0
CB B:MET80 3.9 35.0 1.0
CG B:MET80 3.9 39.7 1.0
C5 B:1QG401 4.1 36.7 1.0
N B:MET82 4.1 32.8 1.0
CA B:LYS38 4.2 31.0 1.0
CE B:MET82 4.3 38.4 1.0
O B:ALA36 4.3 30.9 1.0
N B:VAL81 4.4 30.4 1.0
CA B:MET80 4.4 33.5 1.0
C B:VAL81 4.5 35.6 1.0
SD B:MET80 4.5 45.0 1.0
H6 B:1QG401 4.5 37.8 0.0
H9 B:1QG401 4.5 35.5 0.0
CA B:MET82 4.5 32.7 1.0
C B:ILE37 4.6 37.7 1.0
CD B:LYS38 4.6 40.6 1.0
CG B:LYS38 4.6 36.0 1.0
CG B:MET82 4.7 38.0 1.0
CA B:VAL81 4.7 30.1 1.0
SD B:MET82 4.8 41.3 1.0
CA B:ILE37 4.8 32.7 1.0
C B:ALA36 4.9 32.2 1.0

Fluorine binding site 3 out of 4 in 4kbk

Go back to Fluorine Binding Sites List in 4kbk
Fluorine binding site 3 out of 4 in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:38.0
occ:1.00
 F1 C:1QG401 0.0 38.0 1.0
C8 C:1QG401 1.3 38.0 1.0
C7 C:1QG401 2.4 37.0 1.0
C9 C:1QG401 2.4 33.2 1.0
H7 C:1QG401 2.6 37.7 0.0
H8 C:1QG401 2.6 33.0 0.0
O C:MET80 3.3 31.9 1.0
CE C:MET80 3.3 39.2 1.0
CB C:LYS38 3.5 31.5 1.0
CB C:MET82 3.6 29.2 1.0
C6 C:1QG401 3.6 37.4 1.0
C10 C:1QG401 3.6 33.4 1.0
CG C:MET80 3.7 38.2 1.0
C C:MET80 3.8 32.7 1.0
N C:LYS38 3.9 31.4 1.0
CB C:MET80 3.9 33.7 1.0
C5 C:1QG401 4.1 35.2 1.0
N C:MET82 4.1 28.0 1.0
CE C:MET82 4.2 33.0 1.0
SD C:MET80 4.2 43.6 1.0
O C:ALA36 4.3 30.4 1.0
CA C:LYS38 4.3 31.0 1.0
N C:VAL81 4.4 27.0 1.0
CA C:MET80 4.5 32.0 1.0
C C:VAL81 4.5 31.9 1.0
H6 C:1QG401 4.5 37.7 0.0
H9 C:1QG401 4.5 32.7 0.0
CA C:MET82 4.5 27.7 1.0
CD C:LYS38 4.6 43.9 1.0
CG C:LYS38 4.6 34.6 1.0
C C:ILE37 4.6 36.3 1.0
CG C:MET82 4.6 33.3 1.0
CD1 C:ILE68 4.7 37.0 1.0
SD C:MET82 4.7 37.0 1.0
CA C:VAL81 4.7 26.5 1.0
CA C:ILE37 4.9 31.2 1.0
C C:ALA36 4.9 31.5 1.0

Fluorine binding site 4 out of 4 in 4kbk

Go back to Fluorine Binding Sites List in 4kbk
Fluorine binding site 4 out of 4 in the CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of CK1D in Complex with (3S)-3-{4-[3-(4-Fluorophenyl)-1-Methyl-1H- Pyrazol-4-Yl]Pyridin-2-Yl}Morpholine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:53.6
occ:1.00
 F1 D:1QG401 0.0 53.6 1.0
C8 D:1QG401 1.3 50.7 1.0
C7 D:1QG401 2.3 49.6 1.0
C9 D:1QG401 2.4 48.7 1.0
H7 D:1QG401 2.6 49.9 0.0
H8 D:1QG401 2.6 48.9 0.0
CE D:MET80 3.2 45.9 1.0
CB D:MET82 3.4 32.4 1.0
O D:MET80 3.6 37.0 1.0
C6 D:1QG401 3.6 51.1 1.0
C10 D:1QG401 3.6 49.0 1.0
CB D:LYS38 3.7 39.1 1.0
CE D:MET82 3.9 38.9 1.0
CG D:MET80 4.0 44.3 1.0
N D:LYS38 4.0 37.8 1.0
C D:MET80 4.0 37.6 1.0
CB D:MET80 4.0 40.0 1.0
C5 D:1QG401 4.1 48.6 1.0
N D:MET82 4.1 30.9 1.0
O D:ALA36 4.3 34.6 1.0
CA D:MET82 4.4 29.9 1.0
SD D:MET80 4.4 50.4 1.0
CG D:MET82 4.4 36.7 1.0
SD D:MET82 4.4 42.0 1.0
CA D:LYS38 4.5 37.6 1.0
H6 D:1QG401 4.5 51.0 0.0
H9 D:1QG401 4.5 48.7 0.0
C D:VAL81 4.5 34.2 1.0
N D:VAL81 4.6 32.4 1.0
CA D:MET80 4.7 37.2 1.0
CD D:LYS38 4.7 51.9 1.0
C D:ILE37 4.7 40.5 1.0
CA D:VAL81 4.8 30.7 1.0
CG D:LYS38 4.8 44.0 1.0
C D:ALA36 4.9 35.4 1.0
CA D:ILE37 5.0 35.1 1.0

Reference:

S.Mente, E.Arnold, T.Butler, S.Chakrapani, R.Chandrasekaran, K.Cherry, K.Dirico, A.Doran, K.Fisher, P.Galatsis, M.Green, M.Hayward, J.Humphrey, J.Knafels, J.Li, S.Liu, M.Marconi, S.Mcdonald, J.Ohren, V.Paradis, B.Sneed, K.Walton, T.Wager. Ligand-Protein Interactions of Selective Casein Kinase 1 Delta Inhibitors. J.Med.Chem. V. 56 6819 2013.
ISSN: ISSN 0022-2623
PubMed: 23919824
DOI: 10.1021/JM4006324
Page generated: Sun Dec 13 12:06:13 2020

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