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
Go back to
Fluorine Binding Sites List in 6es0
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: Thu Aug 1 19:45:25 2024
|