Fluorine in PDB 6es0: Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35

Enzymatic activity of Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35

All present enzymatic activity of Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35:
2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35, PDB code: 6es0 was solved by D.M.Pinkas, J.C.Bufton, C.Suebsuwong, S.S.Ray, B.Dai, J.A.Newman, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Degterev, G.D.Cuny, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.74 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.980, 83.740, 139.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35 (pdb code 6es0). 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 the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35, PDB code: 6es0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6es0

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Fluorine binding site 1 out of 4 in the Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35


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 the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.9
occ:1.00
 F17 A:BW8401 0.0 24.9 1.0
C15 A:BW8401 1.4 28.2 1.0
C14 A:BW8401 2.4 23.7 1.0
C16 A:BW8401 2.4 25.6 1.0
N18 A:BW8401 2.7 27.4 1.0
CG2 A:THR95 3.3 20.4 1.0
CB A:LYS47 3.4 23.3 1.0
CG2 A:ILE93 3.6 26.2 1.0
C13 A:BW8401 3.6 26.3 1.0
C11 A:BW8401 3.7 25.6 1.0
CD A:LYS47 3.7 33.4 1.0
C19 A:BW8401 4.0 27.3 1.0
CB A:ILE93 4.0 25.7 1.0
C12 A:BW8401 4.1 29.1 1.0
O A:ILE93 4.2 24.9 1.0
CG A:LYS47 4.2 30.6 1.0
OG1 A:THR95 4.4 21.7 1.0
CB A:THR95 4.4 26.4 1.0
N A:LYS47 4.6 28.4 1.0
CA A:LYS47 4.6 21.4 1.0
CD2 A:LEU70 4.6 27.3 1.0
CD2 A:LEU79 4.7 21.3 1.0
C A:ILE93 4.7 27.2 1.0
O33 A:BW8401 4.7 24.9 1.0
N20 A:BW8401 4.7 33.7 1.0
O10 A:BW8401 4.8 26.0 1.0
OE2 A:GLU66 4.8 34.8 1.0
CD1 A:ILE93 4.9 33.2 1.0
CA A:ILE93 5.0 21.3 1.0

Fluorine binding site 2 out of 4 in 6es0

Go back to Fluorine Binding Sites List in 6es0
Fluorine binding site 2 out of 4 in the Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35


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 the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.1
occ:1.00
 F27 A:BW8401 0.0 34.1 1.0
C25 A:BW8401 1.4 39.0 1.0
C26 A:BW8401 2.4 36.4 1.0
C24 A:BW8401 2.4 46.8 1.0
S28 A:BW8401 3.0 58.9 1.0
C29 A:BW8401 3.3 42.8 1.0
C21 A:BW8401 3.6 38.1 1.0
C23 A:BW8401 3.7 46.8 1.0
O A:ILE162 3.8 21.3 1.0
C30 A:BW8401 3.9 54.7 1.0
O31 A:BW8401 3.9 51.0 1.0
CG2 A:ILE162 4.1 26.1 1.0
C22 A:BW8401 4.1 41.0 1.0
CA A:ALA163 4.2 22.3 1.0
C A:ILE162 4.3 20.7 1.0
C A:ALA163 4.3 26.2 1.0
N A:ALA163 4.4 16.6 1.0
O A:ALA163 4.5 27.9 1.0
CD2 A:HIS144 4.5 35.5 1.0
CG2 A:ILE78 4.5 25.4 1.0
CD1 A:LEU70 4.6 27.6 1.0
NE2 A:HIS144 4.7 34.8 1.0
N A:ASP164 4.7 28.3 1.0
CD1 A:LEU135 4.7 25.4 1.0
CB A:ASP164 4.8 35.0 1.0
O33 A:BW8401 4.8 24.9 1.0
O32 A:BW8401 4.8 56.8 1.0
N20 A:BW8401 4.9 33.7 1.0
CB A:ILE162 5.0 27.4 1.0

Fluorine binding site 3 out of 4 in 6es0

Go back to Fluorine Binding Sites List in 6es0
Fluorine binding site 3 out of 4 in the Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35


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 the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:30.4
occ:1.00
 F17 B:BW8401 0.0 30.4 1.0
C15 B:BW8401 1.4 22.1 1.0
C16 B:BW8401 2.4 22.7 1.0
C14 B:BW8401 2.4 23.2 1.0
N18 B:BW8401 2.8 24.1 1.0
CB B:LYS47 3.5 30.6 1.0
CD B:LYS47 3.6 33.7 1.0
CG2 B:THR95 3.6 22.5 1.0
C11 B:BW8401 3.6 27.2 1.0
C13 B:BW8401 3.6 22.0 1.0
CG2 B:ILE93 3.8 36.4 1.0
C19 B:BW8401 4.1 26.5 1.0
CB B:ILE93 4.1 35.8 1.0
O B:ILE93 4.1 31.6 1.0
C12 B:BW8401 4.1 18.7 1.0
CG B:LYS47 4.2 34.9 1.0
OG1 B:THR95 4.3 27.9 1.0
OE2 B:GLU66 4.6 30.8 1.0
CB B:THR95 4.6 29.0 1.0
N B:LYS47 4.6 35.3 1.0
C B:ILE93 4.6 32.2 1.0
CA B:LYS47 4.6 38.0 1.0
O10 B:BW8401 4.8 29.0 1.0
O33 B:BW8401 4.8 30.8 1.0
CD2 B:LEU79 4.8 26.1 1.0
N20 B:BW8401 4.9 25.4 1.0
CE B:LYS47 4.9 34.7 1.0
CA B:ILE93 5.0 34.0 1.0

Fluorine binding site 4 out of 4 in 6es0

Go back to Fluorine Binding Sites List in 6es0
Fluorine binding site 4 out of 4 in the Crystal Structure of the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35


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 the Kinase Domain of Human RIPK2 in Complex with the Activation Loop Targeting Inhibitor Cs-R35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:36.8
occ:1.00
 F27 B:BW8401 0.0 36.8 1.0
C25 B:BW8401 1.4 38.9 1.0
C24 B:BW8401 2.4 46.6 1.0
C26 B:BW8401 2.4 32.5 1.0
S28 B:BW8401 3.0 53.0 1.0
C23 B:BW8401 3.6 38.2 1.0
C21 B:BW8401 3.7 29.1 1.0
O32 B:BW8401 3.7 44.7 1.0
O B:ILE162 3.8 28.6 1.0
CG2 B:ILE162 4.1 27.2 1.0
C B:ALA163 4.1 30.5 1.0
CA B:ALA163 4.1 20.9 1.0
CD2 B:HIS144 4.1 32.5 1.0
C22 B:BW8401 4.1 32.5 1.0
C B:ILE162 4.2 31.2 1.0
O B:ALA163 4.2 25.8 1.0
NE2 B:HIS144 4.3 27.6 1.0
N B:ALA163 4.3 26.7 1.0
CG2 B:ILE78 4.4 18.5 1.0
C29 B:BW8401 4.5 45.3 1.0
C30 B:BW8401 4.5 51.0 1.0
N B:ASP164 4.6 32.0 1.0
CD1 B:LEU70 4.6 27.4 1.0
CB B:ASP164 4.6 26.5 1.0
O33 B:BW8401 4.8 30.8 1.0
CB B:ILE162 4.8 30.4 1.0
N20 B:BW8401 4.9 25.4 1.0
CD1 B:LEU135 5.0 20.7 1.0

Reference:

C.Suebsuwong, D.M.Pinkas, S.S.Ray, J.C.Bufton, B.Dai, A.N.Bullock, A.Degterev, G.D.Cuny. Activation Loop Targeting Strategy For Design of Receptor-Interacting Protein Kinase 2 (RIPK2) Inhibitors. Bioorg. Med. Chem. Lett. V. 28 577 2018.
ISSN: ESSN 1464-3405
PubMed: 29409752
DOI: 10.1016/J.BMCL.2018.01.044
Page generated: Sun Dec 13 12:49:38 2020

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