Fluorine in PDB 8b94: Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
Protein crystallography data
The structure of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist, PDB code: 8b94
was solved by
A.Friberg,
D.L.Orsi,
E.Pook,
S.Siegel,
C.T.Lemke,
T.Stellfeld,
V.Puetter,
J.Goldstein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.10 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.444,
85.896,
121.271,
90,
90,
90
|
R / Rfree (%)
|
21.2 /
24
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
(pdb code 8b94). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist, PDB code: 8b94:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 1 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:34.3
occ:1.00
|
F1
|
A:Q5O501
|
0.0
|
34.3
|
1.0
|
C6
|
A:Q5O501
|
1.3
|
37.5
|
1.0
|
C1
|
A:Q5O501
|
2.4
|
35.0
|
1.0
|
C5
|
A:Q5O501
|
2.4
|
31.3
|
1.0
|
N2
|
A:Q5O501
|
2.7
|
37.5
|
1.0
|
C16
|
A:Q5O501
|
2.8
|
39.1
|
1.0
|
OE1
|
A:GLN286
|
3.2
|
62.5
|
1.0
|
CZ
|
A:PHE282
|
3.2
|
39.4
|
1.0
|
CE1
|
A:PHE282
|
3.4
|
36.2
|
1.0
|
CD2
|
A:LEU453
|
3.6
|
39.7
|
1.0
|
C2
|
A:Q5O501
|
3.6
|
32.5
|
1.0
|
C4
|
A:Q5O501
|
3.6
|
33.0
|
1.0
|
O3
|
A:Q5O501
|
3.9
|
33.7
|
1.0
|
C17
|
A:Q5O501
|
4.1
|
37.3
|
1.0
|
CE2
|
A:PHE282
|
4.1
|
36.7
|
1.0
|
CA
|
A:GLN286
|
4.1
|
33.2
|
1.0
|
CB
|
A:GLN286
|
4.1
|
39.0
|
1.0
|
C3
|
A:Q5O501
|
4.1
|
31.5
|
1.0
|
CZ
|
A:PHE363
|
4.2
|
37.2
|
1.0
|
CD
|
A:GLN286
|
4.3
|
55.4
|
1.0
|
CD1
|
A:PHE282
|
4.4
|
38.8
|
1.0
|
N
|
A:GLN286
|
4.4
|
32.7
|
1.0
|
CE1
|
A:PHE363
|
4.7
|
37.5
|
1.0
|
CG
|
A:GLN286
|
4.8
|
50.3
|
1.0
|
O
|
A:PHE282
|
4.8
|
33.4
|
1.0
|
CG
|
A:LEU453
|
4.9
|
39.2
|
1.0
|
CD2
|
A:PHE282
|
4.9
|
34.5
|
1.0
|
C
|
A:CYS285
|
4.9
|
31.2
|
1.0
|
CD1
|
A:LEU453
|
5.0
|
42.1
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 2 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:52.9
occ:1.00
|
F2
|
A:Q5O501
|
0.0
|
52.9
|
1.0
|
C15
|
A:Q5O501
|
1.3
|
47.5
|
1.0
|
O1
|
A:Q5O501
|
2.2
|
34.4
|
1.0
|
F3
|
A:Q5O501
|
2.2
|
49.8
|
1.0
|
O
|
A:HOH793
|
2.7
|
36.2
|
1.0
|
C11
|
A:Q5O501
|
2.9
|
29.8
|
1.0
|
C10
|
A:Q5O501
|
3.0
|
27.8
|
1.0
|
NH1
|
A:ARG288
|
3.8
|
42.6
|
1.0
|
CB
|
A:ALA292
|
3.8
|
28.2
|
1.0
|
CB
|
A:MET329
|
3.9
|
29.6
|
1.0
|
C12
|
A:Q5O501
|
4.2
|
29.2
|
1.0
|
O
|
A:ILE326
|
4.3
|
22.4
|
0.4
|
C9
|
A:Q5O501
|
4.3
|
31.3
|
1.0
|
CZ
|
A:ARG288
|
4.4
|
37.6
|
1.0
|
CA
|
A:ILE326
|
4.6
|
23.1
|
0.4
|
O
|
A:HOH703
|
4.6
|
36.4
|
1.0
|
CG2
|
A:ILE326
|
4.7
|
23.1
|
0.4
|
SD
|
A:MET329
|
4.7
|
37.4
|
1.0
|
CG1
|
A:ILE326
|
4.7
|
26.9
|
0.6
|
C
|
A:MET329
|
4.8
|
24.3
|
1.0
|
CG
|
A:MET329
|
4.8
|
33.8
|
1.0
|
N
|
A:LEU330
|
4.8
|
22.2
|
1.0
|
NH2
|
A:ARG288
|
4.8
|
42.8
|
1.0
|
CG1
|
A:ILE326
|
4.9
|
24.6
|
0.4
|
O
|
A:ILE326
|
4.9
|
20.7
|
0.6
|
C
|
A:ILE326
|
4.9
|
20.9
|
0.4
|
CA
|
A:ILE326
|
4.9
|
22.2
|
0.6
|
NE
|
A:ARG288
|
4.9
|
35.9
|
1.0
|
CA
|
A:MET329
|
4.9
|
24.9
|
1.0
|
CB
|
A:ILE326
|
4.9
|
22.8
|
0.4
|
CA
|
A:ALA292
|
5.0
|
27.4
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 3 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:49.8
occ:1.00
|
F3
|
A:Q5O501
|
0.0
|
49.8
|
1.0
|
C15
|
A:Q5O501
|
1.4
|
47.5
|
1.0
|
O1
|
A:Q5O501
|
2.1
|
34.4
|
1.0
|
F2
|
A:Q5O501
|
2.2
|
52.9
|
1.0
|
C11
|
A:Q5O501
|
3.0
|
29.8
|
1.0
|
N
|
A:LEU330
|
3.0
|
22.2
|
1.0
|
C
|
A:MET329
|
3.1
|
24.3
|
1.0
|
CA
|
A:LEU330
|
3.4
|
24.2
|
1.0
|
CB
|
A:MET329
|
3.5
|
29.6
|
1.0
|
O
|
A:ILE326
|
3.5
|
22.4
|
0.4
|
O
|
A:MET329
|
3.5
|
23.9
|
1.0
|
C10
|
A:Q5O501
|
3.7
|
27.8
|
1.0
|
O
|
A:HOH703
|
3.7
|
36.4
|
1.0
|
CD1
|
A:LEU330
|
3.8
|
34.2
|
1.0
|
CA
|
A:MET329
|
3.9
|
24.9
|
1.0
|
C12
|
A:Q5O501
|
3.9
|
29.2
|
1.0
|
O
|
A:ILE326
|
4.0
|
20.7
|
0.6
|
CB
|
A:LEU330
|
4.0
|
26.4
|
1.0
|
CD1
|
A:LEU333
|
4.1
|
27.4
|
1.0
|
O
|
A:HOH793
|
4.2
|
36.2
|
1.0
|
CG
|
A:LEU330
|
4.4
|
37.8
|
1.0
|
C
|
A:ILE326
|
4.6
|
20.9
|
0.4
|
CG
|
A:LEU333
|
4.7
|
24.9
|
1.0
|
C
|
A:LEU330
|
4.7
|
22.0
|
1.0
|
N
|
A:MET329
|
4.7
|
23.3
|
1.0
|
CG2
|
A:ILE326
|
4.9
|
23.1
|
0.4
|
CG
|
A:MET329
|
4.9
|
33.8
|
1.0
|
C9
|
A:Q5O501
|
4.9
|
31.3
|
1.0
|
CA
|
A:ILE326
|
4.9
|
23.1
|
0.4
|
C
|
A:ILE326
|
5.0
|
20.8
|
0.6
|
|
Fluorine binding site 4 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 4 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:52.0
occ:1.00
|
F4
|
A:Q5O501
|
0.0
|
52.0
|
1.0
|
C21
|
A:Q5O501
|
1.4
|
44.3
|
1.0
|
C20
|
A:Q5O501
|
2.4
|
44.2
|
1.0
|
C22
|
A:Q5O501
|
2.4
|
42.0
|
1.0
|
CD1
|
C:ILE2353
|
2.9
|
49.3
|
1.0
|
C19
|
A:Q5O501
|
3.6
|
40.4
|
1.0
|
C23
|
A:Q5O501
|
3.7
|
41.7
|
1.0
|
CD1
|
C:LEU2350
|
3.7
|
44.5
|
1.0
|
CA
|
C:LEU2350
|
3.7
|
40.2
|
1.0
|
CG2
|
A:VAL290
|
3.8
|
31.0
|
1.0
|
N
|
C:LEU2350
|
4.1
|
42.7
|
1.0
|
C18
|
A:Q5O501
|
4.1
|
40.2
|
1.0
|
CG1
|
C:ILE2353
|
4.2
|
43.4
|
1.0
|
CB
|
C:LEU2350
|
4.3
|
41.9
|
1.0
|
C
|
C:GLY2349
|
4.4
|
42.2
|
1.0
|
CB
|
C:ILE2353
|
4.4
|
42.3
|
1.0
|
CG2
|
A:VAL293
|
4.4
|
31.1
|
1.0
|
CA
|
A:VAL290
|
4.5
|
28.4
|
1.0
|
O
|
C:GLY2349
|
4.5
|
43.0
|
1.0
|
NE2
|
A:GLN286
|
4.6
|
57.9
|
1.0
|
CB
|
A:VAL290
|
4.6
|
31.5
|
1.0
|
CG
|
C:LEU2350
|
4.7
|
43.0
|
1.0
|
CG2
|
C:ILE2353
|
4.8
|
45.4
|
1.0
|
C
|
C:LEU2350
|
4.9
|
40.7
|
1.0
|
CB
|
A:VAL293
|
4.9
|
29.7
|
1.0
|
O
|
C:LEU2350
|
4.9
|
38.0
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 5 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:34.5
occ:1.00
|
F1
|
B:Q5O501
|
0.0
|
34.5
|
1.0
|
C6
|
B:Q5O501
|
1.3
|
31.9
|
1.0
|
C1
|
B:Q5O501
|
2.3
|
31.6
|
1.0
|
C5
|
B:Q5O501
|
2.4
|
30.0
|
1.0
|
OE1
|
B:GLN286
|
2.5
|
60.0
|
1.0
|
N2
|
B:Q5O501
|
2.7
|
35.1
|
1.0
|
C16
|
B:Q5O501
|
2.8
|
31.9
|
1.0
|
CZ
|
B:PHE282
|
3.2
|
38.1
|
1.0
|
CE1
|
B:PHE282
|
3.4
|
36.8
|
1.0
|
CD2
|
B:LEU453
|
3.5
|
30.6
|
1.0
|
C2
|
B:Q5O501
|
3.6
|
34.0
|
1.0
|
C4
|
B:Q5O501
|
3.7
|
33.7
|
1.0
|
CD
|
B:GLN286
|
3.7
|
57.0
|
1.0
|
O3
|
B:Q5O501
|
3.9
|
31.0
|
1.0
|
C17
|
B:Q5O501
|
4.0
|
37.1
|
1.0
|
CB
|
B:GLN286
|
4.1
|
40.1
|
1.0
|
CA
|
B:GLN286
|
4.1
|
36.9
|
1.0
|
CE2
|
B:PHE282
|
4.1
|
40.1
|
1.0
|
C3
|
B:Q5O501
|
4.1
|
32.6
|
1.0
|
CZ
|
B:PHE363
|
4.3
|
38.9
|
1.0
|
CD1
|
B:PHE282
|
4.4
|
35.1
|
1.0
|
N
|
B:GLN286
|
4.5
|
35.6
|
1.0
|
CG
|
B:GLN286
|
4.5
|
47.0
|
1.0
|
NE2
|
B:GLN286
|
4.6
|
61.6
|
1.0
|
CG
|
B:LEU453
|
4.8
|
31.8
|
1.0
|
O
|
B:PHE282
|
4.9
|
33.7
|
1.0
|
CD2
|
B:PHE282
|
5.0
|
36.1
|
1.0
|
C18
|
B:Q5O501
|
5.0
|
38.8
|
1.0
|
CD1
|
B:LEU453
|
5.0
|
35.4
|
1.0
|
OG
|
B:SER289
|
5.0
|
28.8
|
0.6
|
CE1
|
B:PHE363
|
5.0
|
42.5
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 6 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:53.4
occ:1.00
|
F2
|
B:Q5O501
|
0.0
|
53.4
|
1.0
|
C15
|
B:Q5O501
|
1.4
|
50.2
|
1.0
|
F3
|
B:Q5O501
|
2.2
|
53.2
|
1.0
|
O1
|
B:Q5O501
|
2.4
|
45.7
|
1.0
|
O
|
B:HOH737
|
2.9
|
42.0
|
1.0
|
C10
|
B:Q5O501
|
3.0
|
40.8
|
1.0
|
C11
|
B:Q5O501
|
3.1
|
43.3
|
1.0
|
CB
|
B:ALA292
|
3.9
|
28.1
|
1.0
|
O
|
B:ILE326
|
4.0
|
23.8
|
1.0
|
NH1
|
B:ARG288
|
4.0
|
44.8
|
1.0
|
CB
|
B:MET329
|
4.1
|
25.3
|
1.0
|
CA
|
B:ILE326
|
4.2
|
21.2
|
1.0
|
CG2
|
B:ILE326
|
4.2
|
24.1
|
1.0
|
C9
|
B:Q5O501
|
4.3
|
33.6
|
1.0
|
C12
|
B:Q5O501
|
4.4
|
38.7
|
1.0
|
N
|
B:LEU330
|
4.5
|
23.2
|
1.0
|
CB
|
B:ILE326
|
4.6
|
22.8
|
1.0
|
C
|
B:ILE326
|
4.6
|
22.8
|
1.0
|
CG1
|
B:ILE326
|
4.6
|
26.3
|
1.0
|
CZ
|
B:ARG288
|
4.6
|
45.2
|
1.0
|
C
|
B:MET329
|
4.8
|
21.4
|
1.0
|
O
|
B:HOH711
|
4.9
|
44.4
|
1.0
|
SD
|
B:MET329
|
5.0
|
33.2
|
1.0
|
CA
|
B:LEU330
|
5.0
|
24.2
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 7 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:53.2
occ:1.00
|
F3
|
B:Q5O501
|
0.0
|
53.2
|
1.0
|
C15
|
B:Q5O501
|
1.4
|
50.2
|
1.0
|
O1
|
B:Q5O501
|
2.2
|
45.7
|
1.0
|
F2
|
B:Q5O501
|
2.2
|
53.4
|
1.0
|
N
|
B:LEU330
|
3.2
|
23.2
|
1.0
|
CA
|
B:LEU330
|
3.3
|
24.2
|
1.0
|
C11
|
B:Q5O501
|
3.3
|
43.3
|
1.0
|
C
|
B:MET329
|
3.4
|
21.4
|
1.0
|
O
|
B:MET329
|
3.6
|
24.5
|
1.0
|
O
|
B:HOH711
|
3.7
|
44.4
|
1.0
|
CB
|
B:LEU330
|
3.8
|
27.7
|
1.0
|
CB
|
B:MET329
|
3.8
|
25.3
|
1.0
|
CD1
|
B:LEU333
|
4.0
|
31.1
|
1.0
|
C10
|
B:Q5O501
|
4.0
|
40.8
|
1.0
|
O
|
B:ILE326
|
4.0
|
23.8
|
1.0
|
CD1
|
B:LEU330
|
4.0
|
30.1
|
1.0
|
CA
|
B:MET329
|
4.2
|
22.3
|
1.0
|
C12
|
B:Q5O501
|
4.3
|
38.7
|
1.0
|
O
|
B:HOH737
|
4.4
|
42.0
|
1.0
|
CG
|
B:LEU333
|
4.5
|
30.1
|
1.0
|
CG
|
B:LEU330
|
4.5
|
30.9
|
1.0
|
NH1
|
B:ARG288
|
4.6
|
44.8
|
1.0
|
C
|
B:LEU330
|
4.6
|
25.2
|
1.0
|
O
|
B:HOH613
|
4.7
|
50.8
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 8b94
Go back to
Fluorine Binding Sites List in 8b94
Fluorine binding site 8 out
of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:48.7
occ:1.00
|
F4
|
B:Q5O501
|
0.0
|
48.7
|
1.0
|
C21
|
B:Q5O501
|
1.4
|
46.5
|
1.0
|
C20
|
B:Q5O501
|
2.4
|
42.0
|
1.0
|
C22
|
B:Q5O501
|
2.4
|
44.8
|
1.0
|
CD1
|
D:ILE2353
|
3.1
|
49.1
|
1.0
|
CD1
|
D:LEU2350
|
3.6
|
45.6
|
1.0
|
C19
|
B:Q5O501
|
3.6
|
37.7
|
1.0
|
C23
|
B:Q5O501
|
3.7
|
43.4
|
1.0
|
CG2
|
B:VAL290
|
3.8
|
39.1
|
1.0
|
CG2
|
B:VAL293
|
4.0
|
29.5
|
1.0
|
CA
|
D:LEU2350
|
4.1
|
43.4
|
1.0
|
C18
|
B:Q5O501
|
4.2
|
38.8
|
1.0
|
CA
|
B:VAL290
|
4.3
|
32.2
|
1.0
|
CG1
|
D:ILE2353
|
4.3
|
47.0
|
1.0
|
CB
|
D:ILE2353
|
4.3
|
41.7
|
1.0
|
CG2
|
D:ILE2353
|
4.3
|
43.0
|
1.0
|
CB
|
B:VAL293
|
4.5
|
26.3
|
1.0
|
CB
|
D:LEU2350
|
4.5
|
45.5
|
1.0
|
CB
|
B:VAL290
|
4.5
|
34.6
|
1.0
|
CG
|
D:LEU2350
|
4.7
|
45.5
|
1.0
|
CG1
|
B:VAL293
|
4.7
|
29.5
|
1.0
|
N
|
D:LEU2350
|
4.7
|
47.5
|
1.0
|
N
|
B:VAL290
|
4.8
|
29.2
|
1.0
|
CG1
|
B:VAL290
|
4.9
|
35.1
|
1.0
|
NE2
|
B:GLN286
|
4.9
|
61.6
|
1.0
|
O
|
B:SER289
|
5.0
|
28.9
|
0.4
|
|
Reference:
D.L.Orsi,
S.J.Ferrara,
S.Siegel,
A.Friberg,
L.Bouche,
E.Pook,
P.Lienau,
J.P.Bluck,
C.T.Lemke,
G.Akcay,
T.Stellfeld,
H.Meyer,
V.Putter,
S.J.Holton,
D.Korr,
I.Jerchel-Furau,
C.Pantelidou,
C.A.Strathdee,
M.Meyerson,
K.Eis,
J.T.Goldstein.
Discovery and Characterization of Orally Bioavailable 4-Chloro-6-Fluoroisophthalamides As Covalent Pparg Inverse-Agonists. Bioorg.Med.Chem. V. 78 17130 2022.
ISSN: ESSN 1464-3391
PubMed: 36542958
DOI: 10.1016/J.BMC.2022.117130
Page generated: Fri Aug 2 16:45:05 2024
|