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Fluorine in PDB 4c8b: Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib

Enzymatic activity of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib

All present enzymatic activity of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib:
2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib, PDB code: 4c8b was solved by P.Canning, T.Krojer, A.Bradley, P.Mahajan, S.Goubin, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.06 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.735, 86.682, 137.335, 90.00, 90.00, 90.00
R / Rfree (%) 20.061 / 24.361

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib (pdb code 4c8b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib, PDB code: 4c8b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 1 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:50.0
occ:1.00
 F1 A:0LI1000 0.0 50.0 1.0
C19 A:0LI1000 1.3 48.3 1.0
F2 A:0LI1000 2.1 52.2 1.0
F3 A:0LI1000 2.2 44.4 1.0
C17 A:0LI1000 2.3 41.9 1.0
C16 A:0LI1000 2.8 41.9 1.0
C20 A:0LI1000 2.8 42.1 1.0
C18 A:0LI1000 3.4 42.9 1.0
CG2 A:ILE78 4.0 41.6 1.0
C15 A:0LI1000 4.1 43.3 1.0
CD2 A:LEU135 4.2 47.5 1.0
CD2 A:LEU70 4.3 50.2 1.0
N3 A:0LI1000 4.3 43.9 1.0
CD1 A:LEU135 4.4 46.5 1.0
C13 A:0LI1000 4.6 41.5 1.0
CB A:ALA73 4.8 50.7 1.0
CD1 A:ILE78 4.9 41.0 1.0
CG2 A:ILE69 4.9 56.0 1.0
C14 A:0LI1000 4.9 41.5 1.0
CG A:LEU135 5.0 47.1 1.0

Fluorine binding site 2 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 2 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:52.2
occ:1.00
 F2 A:0LI1000 0.0 52.2 1.0
C19 A:0LI1000 1.3 48.3 1.0
F1 A:0LI1000 2.1 50.0 1.0
F3 A:0LI1000 2.2 44.4 1.0
C17 A:0LI1000 2.4 41.9 1.0
C18 A:0LI1000 2.7 42.9 1.0
O A:ILE162 3.2 42.8 1.0
CG2 A:ILE78 3.5 41.6 1.0
CD2 A:LEU70 3.6 50.2 1.0
C16 A:0LI1000 3.6 41.9 1.0
CA A:ALA163 3.8 43.0 1.0
C A:ILE162 3.8 42.5 1.0
N A:ALA163 4.1 42.2 1.0
C13 A:0LI1000 4.1 41.5 1.0
C A:ALA163 4.2 43.8 1.0
C20 A:0LI1000 4.3 42.1 1.0
CG2 A:ILE162 4.4 44.2 1.0
O1 A:0LI1000 4.4 42.4 1.0
N A:LEU79 4.6 42.5 1.0
CG A:LEU70 4.6 50.6 1.0
O A:ALA163 4.6 42.6 1.0
N A:ASP164 4.7 45.3 1.0
C15 A:0LI1000 4.8 43.3 1.0
CB A:ILE78 4.8 41.5 1.0
CD1 A:ILE78 4.8 41.0 1.0
CB A:ILE162 4.8 43.5 1.0
CB A:LEU79 4.9 43.1 1.0
N2 A:0LI1000 4.9 39.9 1.0
CA A:ILE162 5.0 43.0 1.0
CB A:ALA163 5.0 42.7 1.0
C14 A:0LI1000 5.0 41.5 1.0

Fluorine binding site 3 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 3 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:44.4
occ:1.00
 F3 A:0LI1000 0.0 44.4 1.0
C19 A:0LI1000 1.3 48.3 1.0
F2 A:0LI1000 2.2 52.2 1.0
F1 A:0LI1000 2.2 50.0 1.0
C17 A:0LI1000 2.4 41.9 1.0
C16 A:0LI1000 3.1 41.9 1.0
C20 A:0LI1000 3.2 42.1 1.0
CD2 A:HIS144 3.3 46.5 1.0
NE2 A:HIS144 3.3 46.0 1.0
C18 A:0LI1000 3.4 42.9 1.0
CG2 A:ILE162 3.6 44.2 1.0
O A:ALA163 3.7 42.6 1.0
C A:ALA163 3.8 43.8 1.0
CA A:ALA163 4.1 43.0 1.0
N A:ALA163 4.2 42.2 1.0
O A:ILE162 4.3 42.8 1.0
C A:ILE162 4.3 42.5 1.0
C15 A:0LI1000 4.4 43.3 1.0
CG A:HIS144 4.4 46.7 1.0
CB A:ASP164 4.4 46.8 1.0
N A:ASP164 4.4 45.3 1.0
CE1 A:HIS144 4.4 46.0 1.0
N3 A:0LI1000 4.5 43.9 1.0
CD1 A:LEU135 4.5 46.5 1.0
C21 A:0LI1000 4.6 45.4 1.0
C13 A:0LI1000 4.6 41.5 1.0
CB A:ILE162 4.6 43.5 1.0
ND1 A:HIS144 5.0 46.3 1.0

Fluorine binding site 4 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 4 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:45.0
occ:1.00
 F1 B:0LI1000 0.0 45.0 1.0
C19 B:0LI1000 1.3 47.0 1.0
F3 B:0LI1000 2.2 45.8 1.0
F2 B:0LI1000 2.2 48.0 1.0
C17 B:0LI1000 2.3 48.5 1.0
C16 B:0LI1000 2.9 52.1 1.0
C20 B:0LI1000 2.9 52.5 1.0
C18 B:0LI1000 3.5 48.5 1.0
CG2 B:ILE78 3.9 47.1 1.0
CD2 B:LEU135 4.2 53.6 1.0
C15 B:0LI1000 4.2 54.3 1.0
CD1 B:LEU135 4.3 53.9 1.0
CD2 B:LEU70 4.4 54.5 1.0
N3 B:0LI1000 4.4 52.4 1.0
C13 B:0LI1000 4.6 47.7 1.0
CD1 B:ILE78 4.7 48.8 1.0
CB B:ALA73 4.8 57.2 1.0
CG B:LEU135 4.9 53.0 1.0
O B:ILE162 4.9 46.2 1.0
C14 B:0LI1000 4.9 52.6 1.0

Fluorine binding site 5 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 5 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:48.0
occ:1.00
 F2 B:0LI1000 0.0 48.0 1.0
C19 B:0LI1000 1.3 47.0 1.0
F3 B:0LI1000 2.2 45.8 1.0
F1 B:0LI1000 2.2 45.0 1.0
C17 B:0LI1000 2.3 48.5 1.0
C18 B:0LI1000 2.6 48.5 1.0
O B:ILE162 3.0 46.2 1.0
CA B:ALA163 3.4 52.8 1.0
C16 B:0LI1000 3.6 52.1 1.0
C B:ILE162 3.6 47.0 1.0
N B:ALA163 3.8 50.0 1.0
C B:ALA163 3.8 54.3 1.0
CG2 B:ILE78 3.9 47.1 1.0
CD2 B:LEU70 4.0 54.5 1.0
C13 B:0LI1000 4.0 47.7 1.0
CG2 B:ILE162 4.1 47.1 1.0
O1 B:0LI1000 4.2 49.8 1.0
N B:ASP164 4.2 58.2 1.0
O B:ALA163 4.3 54.1 1.0
C20 B:0LI1000 4.3 52.5 1.0
CB B:ILE162 4.6 46.6 1.0
CB B:ALA163 4.6 53.6 1.0
C15 B:0LI1000 4.7 54.3 1.0
N B:LEU79 4.7 49.3 1.0
CA B:ILE162 4.8 46.5 1.0
N2 B:0LI1000 4.8 45.8 1.0
C14 B:0LI1000 4.9 52.6 1.0
C12 B:0LI1000 4.9 46.6 1.0
CB B:LEU79 5.0 49.9 1.0
CD1 B:ILE78 5.0 48.8 1.0
CG B:LEU70 5.0 55.2 1.0

Fluorine binding site 6 out of 6 in 4c8b

Go back to Fluorine Binding Sites List in 4c8b
Fluorine binding site 6 out of 6 in the Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:45.8
occ:1.00
 F3 B:0LI1000 0.0 45.8 1.0
C19 B:0LI1000 1.3 47.0 1.0
F2 B:0LI1000 2.2 48.0 1.0
F1 B:0LI1000 2.2 45.0 1.0
C17 B:0LI1000 2.3 48.5 1.0
C16 B:0LI1000 2.9 52.1 1.0
C20 B:0LI1000 3.0 52.5 1.0
CD2 B:HIS144 3.2 49.4 1.0
NE2 B:HIS144 3.3 49.6 1.0
C18 B:0LI1000 3.3 48.5 1.0
O B:ALA163 3.7 54.1 1.0
CG2 B:ILE162 3.8 47.1 1.0
C B:ALA163 3.8 54.3 1.0
N3 B:0LI1000 4.1 52.4 1.0
C21 B:0LI1000 4.2 52.9 1.0
C15 B:0LI1000 4.2 54.3 1.0
CB B:ASP164 4.2 61.8 1.0
CA B:ALA163 4.2 52.8 1.0
N B:ASP164 4.3 58.2 1.0
CG B:HIS144 4.3 49.7 1.0
CE1 B:HIS144 4.4 49.8 1.0
N B:ALA163 4.4 50.0 1.0
C13 B:0LI1000 4.5 47.7 1.0
CD1 B:LEU135 4.5 53.9 1.0
O B:ILE162 4.5 46.2 1.0
C B:ILE162 4.6 47.0 1.0
C14 B:0LI1000 4.8 52.6 1.0
CA B:ASP164 4.9 60.1 1.0
ND1 B:HIS144 4.9 49.7 1.0
CB B:ILE162 4.9 46.6 1.0

Reference:

P.Canning, A.Bullock. Structure of the Kinase Domain of Human RIPK2 in Complex with Ponatinib To Be Published.
Page generated: Thu Aug 1 00:40:40 2024

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