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Fluorine in PDB 6hmp: Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)

Enzymatic activity of Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)

All present enzymatic activity of Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3):
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3), PDB code: 6hmp was solved by C.Pichlo, M.Schehr, J.Charl, E.Brunstein, C.Peifer, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.53 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.819, 72.223, 89.161, 90.00, 103.21, 90.00
R / Rfree (%) 18.5 / 21.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3) (pdb code 6hmp). 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 Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3), PDB code: 6hmp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6hmp

Go back to Fluorine Binding Sites List in 6hmp
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)


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 Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:0.1
occ:1.00
 F31 A:GEW301 0.0 0.1 1.0
C30 A:GEW301 1.4 1.0 1.0
HZ1 A:LYS130 2.3 79.5 1.0
C32 A:GEW301 2.4 0.7 1.0
C29 A:GEW301 2.4 0.8 1.0
H321 A:GEW301 2.6 0.3 1.0
H291 A:GEW301 2.6 0.6 1.0
HZ2 A:LYS130 2.8 79.5 1.0
NZ A:LYS130 2.9 66.2 1.0
HE3 A:LYS130 3.3 71.9 1.0
HZ3 A:LYS130 3.6 79.5 1.0
CE A:LYS130 3.6 59.9 1.0
C28 A:GEW301 3.6 0.9 1.0
C33 A:GEW301 3.7 0.6 1.0
HE2 A:LYS130 4.1 71.9 1.0
C27 A:GEW301 4.1 0.1 1.0
H281 A:GEW301 4.4 0.3 1.0
H331 A:GEW301 4.4 0.7 1.0
HB2 A:ASP132 4.6 45.5 1.0
HD2 A:LYS130 4.9 60.5 1.0
CD A:LYS130 4.9 50.4 1.0
HB3 A:ASP132 4.9 45.5 1.0
O A:SER17 4.9 90.1 1.0

Fluorine binding site 2 out of 4 in 6hmp

Go back to Fluorine Binding Sites List in 6hmp
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)


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 Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:47.5
occ:1.00
 F40 A:GEW301 0.0 47.5 1.0
C39 A:GEW301 1.4 48.8 1.0
C41 A:GEW301 2.4 50.7 1.0
C38 A:GEW301 2.4 46.0 1.0
H411 A:GEW301 2.6 60.8 1.0
H381 A:GEW301 2.6 55.3 1.0
HB2 A:MET82 2.6 39.0 1.0
HE3 A:MET80 2.6 70.7 1.0
HG2 A:MET80 2.8 62.6 1.0
HB3 A:MET80 3.1 58.2 1.0
O A:MET80 3.1 45.1 1.0
HB2 A:LYS38 3.2 58.6 1.0
HB3 A:LYS38 3.3 58.6 1.0
HB3 A:MET82 3.3 39.0 1.0
HE3 A:MET82 3.3 48.0 1.0
CB A:MET82 3.4 32.5 1.0
CE A:MET80 3.4 58.9 1.0
HE2 A:MET80 3.5 70.7 1.0
H A:LYS38 3.5 58.1 1.0
C A:MET80 3.6 46.1 1.0
CG A:MET80 3.6 52.1 1.0
H A:MET82 3.6 46.4 1.0
C42 A:GEW301 3.7 47.0 1.0
C37 A:GEW301 3.7 42.9 1.0
CB A:LYS38 3.7 49.0 1.0
N A:MET82 3.7 38.6 1.0
CB A:MET80 3.7 48.4 1.0
HD12 A:ILE68 3.9 52.5 1.0
N A:LYS38 4.0 48.6 1.0
HA A:VAL81 4.1 52.6 1.0
O A:ALA36 4.1 45.6 1.0
C A:VAL81 4.1 43.2 1.0
N A:VAL81 4.1 46.9 1.0
C36 A:GEW301 4.1 42.9 1.0
CA A:MET82 4.2 34.8 1.0
HE1 A:MET80 4.2 70.7 1.0
CE A:MET82 4.2 40.0 1.0
SD A:MET80 4.3 57.4 1.0
CA A:MET80 4.3 46.5 1.0
CA A:VAL81 4.3 43.8 1.0
HA A:ILE37 4.3 61.1 1.0
HD2 A:LYS38 4.4 59.2 1.0
HG3 A:MET80 4.4 62.6 1.0
H421 A:GEW301 4.4 56.5 1.0
H371 A:GEW301 4.4 51.5 1.0
HD13 A:ILE68 4.5 52.5 1.0
CA A:LYS38 4.5 49.2 1.0
CD1 A:ILE68 4.5 43.7 1.0
CG A:MET82 4.5 33.7 1.0
HA A:MET82 4.5 41.7 1.0
HD3 A:LYS38 4.6 59.2 1.0
HB2 A:MET80 4.6 58.2 1.0
HD11 A:ILE68 4.6 52.5 1.0
SD A:MET82 4.7 36.2 1.0
HE1 A:MET82 4.7 48.0 1.0
H A:VAL81 4.7 56.3 1.0
C A:ILE37 4.7 48.4 1.0
O A:VAL81 4.8 46.0 1.0
C A:ALA36 4.8 44.7 1.0
CD A:LYS38 4.8 49.3 1.0
HG3 A:MET82 4.8 40.5 1.0
HG23 A:ILE68 4.9 50.8 1.0
HE2 A:MET82 4.9 48.0 1.0
CG A:LYS38 4.9 49.5 1.0
CA A:ILE37 4.9 50.9 1.0
H A:MET80 4.9 55.3 1.0
HB3 A:ALA36 4.9 50.1 1.0
HA A:MET80 5.0 55.8 1.0

Fluorine binding site 3 out of 4 in 6hmp

Go back to Fluorine Binding Sites List in 6hmp
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)


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 Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:1.0
occ:0.98
 F31 B:GEW301 0.0 1.0 1.0
C30 B:GEW301 1.4 0.2 1.0
HZ3 B:LYS130 1.7 0.5 1.0
HZ1 B:LYS130 2.1 0.5 1.0
NZ B:LYS130 2.2 87.9 1.0
C32 B:GEW301 2.4 0.9 1.0
C29 B:GEW301 2.4 0.6 1.0
H321 B:GEW301 2.6 0.1 1.0
H291 B:GEW301 2.6 0.9 1.0
HE3 B:LYS130 2.9 85.7 1.0
HZ2 B:LYS130 2.9 0.5 1.0
CE B:LYS130 3.1 71.4 1.0
HE2 B:LYS130 3.6 85.7 1.0
C33 B:GEW301 3.6 0.6 1.0
C28 B:GEW301 3.7 0.4 1.0
C27 B:GEW301 4.2 0.8 1.0
HD2 B:LYS130 4.3 61.2 1.0
CD B:LYS130 4.3 50.9 1.0
H331 B:GEW301 4.4 0.2 1.0
H281 B:GEW301 4.4 0.1 1.0
OD2 B:ASP128 4.5 45.9 1.0
HB2 B:ASP132 4.6 60.9 1.0
HD3 B:LYS130 4.7 61.2 1.0
O B:SER17 4.8 79.2 1.0
HG1 B:THR176 4.9 55.8 1.0

Fluorine binding site 4 out of 4 in 6hmp

Go back to Fluorine Binding Sites List in 6hmp
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3)


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 Casein Kinase I Delta in Complex with A Photoswitchable 2-Azoimidazole-Based Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:0.0
occ:0.98
 F40 B:GEW301 0.0 0.0 1.0
C39 B:GEW301 1.4 0.2 1.0
C38 B:GEW301 2.4 0.8 1.0
C41 B:GEW301 2.4 1.0 1.0
HG3 B:MET82 2.5 54.4 0.2
HE3 B:MET80 2.5 55.0 1.0
H381 B:GEW301 2.6 0.2 1.0
H411 B:GEW301 2.6 0.2 1.0
HB2 B:LYS38 2.9 62.9 1.0
HB3 B:LYS38 2.9 62.9 1.0
HB3 B:MET80 3.0 52.4 1.0
HG2 B:MET80 3.0 52.4 1.0
O B:MET80 3.0 42.0 1.0
HB2 B:MET82 3.1 50.0 0.8
HE2 B:MET80 3.2 55.0 1.0
CE B:MET80 3.3 45.8 1.0
HE3 B:MET82 3.3 62.8 0.8
CG B:MET82 3.3 45.3 0.2
CB B:LYS38 3.4 52.5 1.0
H B:LYS38 3.4 59.4 1.0
HD12 B:ILE68 3.6 86.1 1.0
C37 B:GEW301 3.7 0.1 1.0
C B:MET80 3.7 45.4 1.0
C42 B:GEW301 3.7 0.3 1.0
CG B:MET80 3.7 43.6 1.0
CB B:MET80 3.7 43.6 1.0
HB2 B:MET82 3.7 49.4 0.2
HB3 B:MET82 3.8 50.0 0.8
SD B:MET82 3.8 51.4 0.2
N B:LYS38 3.8 49.6 1.0
CB B:MET82 3.9 41.6 0.8
HE1 B:MET80 4.0 55.0 1.0
HG2 B:MET82 4.0 54.4 0.2
HD2 B:LYS38 4.0 66.3 1.0
CB B:MET82 4.0 41.1 0.2
HD11 B:ILE68 4.1 86.1 1.0
H B:MET82 4.1 48.9 0.2
C36 B:GEW301 4.2 0.4 1.0
CD1 B:ILE68 4.2 71.7 1.0
H B:MET82 4.2 48.8 0.8
N B:MET82 4.2 40.7 0.2
CA B:LYS38 4.2 51.1 1.0
N B:MET82 4.2 40.6 0.8
HD3 B:LYS38 4.2 66.3 1.0
SD B:MET80 4.3 44.2 1.0
CE B:MET82 4.3 52.3 0.8
HD13 B:ILE68 4.3 86.1 1.0
O B:ALA36 4.3 46.5 1.0
CA B:MET80 4.3 46.9 1.0
HA B:VAL81 4.3 57.2 1.0
HA B:ILE37 4.3 56.2 1.0
N B:VAL81 4.3 48.2 1.0
H371 B:GEW301 4.4 0.2 1.0
H421 B:GEW301 4.4 0.2 1.0
C B:VAL81 4.4 43.2 1.0
CD B:LYS38 4.4 55.4 1.0
HB2 B:MET80 4.5 52.4 1.0
CG B:LYS38 4.5 54.2 1.0
HG3 B:MET80 4.5 52.4 1.0
C B:ILE37 4.5 48.4 1.0
CA B:VAL81 4.6 47.6 1.0
CA B:MET82 4.6 39.5 0.2
CA B:MET82 4.6 39.5 0.8
HE1 B:MET82 4.7 62.8 0.8
HD11 B:LEU49 4.7 54.8 1.0
HE2 B:MET82 4.8 62.8 0.8
H B:MET80 4.8 61.5 1.0
HA B:MET82 4.8 47.5 0.2
CA B:ILE37 4.8 47.0 1.0
HA B:LYS38 4.9 61.2 1.0
C B:ALA36 4.9 46.2 1.0
HB3 B:MET82 4.9 49.4 0.2
H B:VAL81 4.9 57.9 1.0
CG B:MET82 5.0 44.3 0.8
HG23 B:ILE68 5.0 85.7 1.0
O B:VAL81 5.0 44.7 1.0

Reference:

M.Schehr, C.Ianes, J.Weisner, L.Heintze, M.P.Muller, C.Pichlo, J.Charl, E.Brunstein, J.Ewert, M.Lehr, U.Baumann, D.Rauh, U.Knippschild, C.Peifer, R.Herges. 2-Azo-, 2-Diazocine-Thiazols and 2-Azo-Imidazoles As Photoswitchable Kinase Inhibitors: Limitations and Pitfalls of the Photoswitchable Inhibitor Approach. Photochem. Photobiol. Sci. V. 18 1398 2019.
ISSN: ISSN 1474-9092
PubMed: 30924488
DOI: 10.1039/C9PP00010K
Page generated: Thu Aug 1 21:15:02 2024

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