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Fluorine in PDB 4kba: CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor

Enzymatic activity of CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor

All present enzymatic activity of CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor:
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor, PDB code: 4kba was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.689, 83.964, 89.290, 108.00, 105.71, 93.00
R / Rfree (%) 20.8 / 23.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor (pdb code 4kba). 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 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor, PDB code: 4kba:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4kba

Go back to Fluorine Binding Sites List in 4kba
Fluorine binding site 1 out of 4 in the CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine 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 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.6
occ:1.00
 F1 A:1QM401 0.0 27.6 1.0
C9 A:1QM401 1.3 30.0 1.0
C10 A:1QM401 2.3 32.3 1.0
C8 A:1QM401 2.4 28.5 1.0
H5 A:1QM401 2.6 32.8 0.0
H4 A:1QM401 2.6 28.5 0.0
O A:MET80 3.4 25.2 1.0
CE A:MET80 3.5 35.0 1.0
CB A:MET82 3.5 28.3 1.0
CB A:LYS38 3.5 26.7 1.0
C11 A:1QM401 3.6 33.6 1.0
C7 A:1QM401 3.6 30.4 1.0
CG A:MET80 3.7 34.2 1.0
N A:LYS38 3.8 25.9 1.0
C A:MET80 3.8 28.4 1.0
N A:MET82 4.0 26.4 1.0
CB A:MET80 4.0 30.5 1.0
O A:ALA36 4.1 25.8 1.0
C6 A:1QM401 4.1 32.2 1.0
SD A:MET80 4.2 38.6 1.0
CA A:LYS38 4.3 25.6 1.0
SD A:MET82 4.3 37.1 1.0
N A:VAL81 4.4 25.8 1.0
C A:VAL81 4.4 29.7 1.0
CA A:MET82 4.4 26.2 1.0
H6 A:1QM401 4.5 33.7 0.0
H3 A:1QM401 4.5 30.0 0.0
C A:ILE37 4.5 29.8 1.0
CG A:MET82 4.5 32.2 1.0
CA A:MET80 4.5 28.9 1.0
CA A:VAL81 4.6 25.3 1.0
C A:ALA36 4.7 27.7 1.0
CA A:ILE37 4.7 26.3 1.0
CG A:LYS38 4.8 30.3 1.0
CD A:LYS38 4.8 32.5 1.0
N A:ILE37 5.0 26.2 1.0

Fluorine binding site 2 out of 4 in 4kba

Go back to Fluorine Binding Sites List in 4kba
Fluorine binding site 2 out of 4 in the CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine 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 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.7
occ:1.00
 F1 B:1QM401 0.0 40.7 1.0
C9 B:1QM401 1.3 40.6 1.0
C8 B:1QM401 2.3 38.9 1.0
C10 B:1QM401 2.4 39.7 1.0
H4 B:1QM401 2.6 39.4 0.0
H5 B:1QM401 2.6 40.0 0.0
CB B:MET82 3.4 27.1 1.0
O B:MET80 3.4 33.4 1.0
C7 B:1QM401 3.6 38.1 1.0
CG B:MET80 3.6 39.9 1.0
C11 B:1QM401 3.6 39.0 1.0
CB B:LYS38 3.6 35.1 1.0
CE B:MET80 3.6 41.8 1.0
C B:MET80 3.8 35.1 1.0
CB B:MET80 3.9 36.1 1.0
N B:LYS38 4.0 34.2 1.0
N B:MET82 4.0 27.3 1.0
O B:ALA36 4.1 33.2 1.0
C6 B:1QM401 4.1 38.7 1.0
CE B:MET82 4.3 31.2 1.0
CA B:MET82 4.3 26.7 1.0
C B:VAL81 4.4 32.8 1.0
SD B:MET82 4.4 34.2 1.0
SD B:MET80 4.4 45.0 1.0
N B:VAL81 4.4 31.5 1.0
CG B:MET82 4.4 29.7 1.0
CA B:LYS38 4.4 34.2 1.0
H3 B:1QM401 4.5 37.9 0.0
H6 B:1QM401 4.5 38.6 0.0
CA B:MET80 4.5 34.0 1.0
CA B:VAL81 4.6 30.4 1.0
C B:ILE37 4.7 36.4 1.0
CD B:LYS38 4.7 34.4 1.0
CG B:LYS38 4.8 35.1 1.0
C B:ALA36 4.8 32.8 1.0
CA B:ILE37 4.9 30.6 1.0

Fluorine binding site 3 out of 4 in 4kba

Go back to Fluorine Binding Sites List in 4kba
Fluorine binding site 3 out of 4 in the CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine 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 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:29.8
occ:1.00
 F1 C:1QM401 0.0 29.8 1.0
C9 C:1QM401 1.3 28.0 1.0
C10 C:1QM401 2.3 26.8 1.0
C8 C:1QM401 2.4 24.6 1.0
H5 C:1QM401 2.6 27.3 0.0
H4 C:1QM401 2.6 24.8 0.0
CE C:MET80 3.3 38.5 1.0
O C:MET80 3.4 28.0 1.0
CB C:MET82 3.4 27.6 1.0
CG C:MET80 3.6 36.4 1.0
C11 C:1QM401 3.6 27.7 1.0
C7 C:1QM401 3.6 25.1 1.0
CB C:LYS38 3.7 22.4 1.0
C C:MET80 3.8 30.1 1.0
N C:MET82 3.9 26.0 1.0
CB C:MET80 3.9 31.6 1.0
N C:LYS38 3.9 24.3 1.0
SD C:MET80 4.0 42.0 1.0
C6 C:1QM401 4.1 26.6 1.0
O C:ALA36 4.1 27.5 1.0
C C:VAL81 4.2 29.4 1.0
SD C:MET82 4.2 37.4 1.0
N C:VAL81 4.3 27.2 1.0
CA C:MET82 4.3 25.7 1.0
CG C:MET82 4.4 31.8 1.0
CA C:VAL81 4.4 27.1 1.0
CA C:LYS38 4.5 22.8 1.0
CA C:MET80 4.5 29.2 1.0
H6 C:1QM401 4.5 27.7 0.0
H3 C:1QM401 4.5 24.7 0.0
C C:ILE37 4.6 28.5 1.0
CA C:ILE37 4.7 24.8 1.0
C C:ALA36 4.8 27.4 1.0
O C:VAL81 4.8 28.1 1.0
CG C:LYS38 5.0 24.1 1.0
CD C:LYS38 5.0 20.9 1.0

Fluorine binding site 4 out of 4 in 4kba

Go back to Fluorine Binding Sites List in 4kba
Fluorine binding site 4 out of 4 in the CK1D in Complex with 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine 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 9-[3-(4-Fluorophenyl)-1-Methyl-1H-Pyrazol-4-Yl]- 2,3,4,5-Tetrahydropyrido[2,3-F][1,4]Oxazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:40.4
occ:1.00
 F1 D:1QM401 0.0 40.4 1.0
C9 D:1QM401 1.3 37.8 1.0
C8 D:1QM401 2.3 37.3 1.0
C10 D:1QM401 2.4 37.1 1.0
H4 D:1QM401 2.6 37.8 0.0
H5 D:1QM401 2.6 37.4 0.0
CE D:MET80 3.4 37.2 0.5
CB D:MET82 3.5 29.6 1.0
O D:MET80 3.5 31.4 1.0
CB D:LYS38 3.6 36.1 1.0
CG D:MET80 3.6 35.1 0.5
C7 D:1QM401 3.6 35.5 1.0
C11 D:1QM401 3.6 38.2 1.0
CE D:MET80 3.7 33.4 0.5
CG D:MET80 3.8 37.9 0.5
SD D:MET80 3.9 41.6 0.5
CB D:MET80 3.9 34.3 0.5
CB D:MET80 3.9 32.9 0.5
C D:MET80 3.9 33.7 1.0
N D:LYS38 4.0 34.4 1.0
CE D:MET82 4.0 32.9 1.0
N D:MET82 4.0 29.4 1.0
C6 D:1QM401 4.1 35.3 1.0
C D:VAL81 4.4 34.9 1.0
O D:ALA36 4.4 32.8 1.0
CA D:MET82 4.4 28.8 1.0
SD D:MET80 4.4 38.4 0.5
CA D:LYS38 4.4 34.4 1.0
N D:VAL81 4.4 31.8 1.0
H3 D:1QM401 4.5 35.2 0.0
H6 D:1QM401 4.5 37.9 0.0
CA D:MET80 4.5 32.6 0.5
CG D:MET82 4.5 32.0 1.0
CA D:MET80 4.5 32.0 0.5
SD D:MET82 4.6 35.7 1.0
CD D:LYS38 4.6 33.8 1.0
CA D:VAL81 4.7 31.1 1.0
CG D:LYS38 4.7 33.5 1.0
C D:ILE37 4.7 38.1 1.0
O D:VAL81 4.9 35.6 1.0
CA D:ILE37 4.9 33.4 1.0
C D:ALA36 4.9 33.7 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 12:06:06 2020

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