Fluorine in PDB 7np5: Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
Protein crystallography data
The structure of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216, PDB code: 7np5
was solved by
G.J.M.Oerlemans,
B.A.Somsen,
R.M.J.M.De Vries,
F.A.Meijer,
L.Brunsveld,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.70 /
1.55
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.223,
108.223,
98.797,
90,
90,
120
|
R / Rfree (%)
|
23.4 /
27
|
Other elements in 7np5:
The structure of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
(pdb code 7np5). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216, PDB code: 7np5:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 7np5
Go back to
Fluorine Binding Sites List in 7np5
Fluorine binding site 1 out
of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
![](/pictures/F/pdb/np/7np5-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/np/7np5-F-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:31.5
occ:1.00
|
F1
|
A:UKB601
|
0.0
|
31.5
|
1.0
|
C15
|
A:UKB601
|
1.3
|
36.1
|
1.0
|
F2
|
A:UKB601
|
2.1
|
38.7
|
1.0
|
F3
|
A:UKB601
|
2.1
|
33.5
|
1.0
|
C14
|
A:UKB601
|
2.4
|
34.3
|
1.0
|
C8
|
A:UKB601
|
2.8
|
27.3
|
1.0
|
C9
|
A:UKB601
|
3.0
|
28.5
|
1.0
|
N1
|
A:UKB601
|
3.1
|
32.4
|
1.0
|
C7
|
A:UKB601
|
3.5
|
27.5
|
1.0
|
NE2
|
A:GLN484
|
3.5
|
37.6
|
1.0
|
C13
|
A:UKB601
|
3.5
|
32.2
|
1.0
|
O
|
A:LEU505
|
3.6
|
33.7
|
1.0
|
CB
|
A:LEU505
|
3.6
|
31.8
|
1.0
|
CD1
|
A:LEU505
|
3.6
|
32.0
|
1.0
|
CZ
|
A:PHE506
|
3.8
|
35.3
|
1.0
|
O4
|
A:UKB601
|
3.8
|
30.6
|
1.0
|
CD
|
A:GLN484
|
4.0
|
45.6
|
1.0
|
CG
|
A:LEU505
|
4.0
|
29.8
|
1.0
|
CE2
|
A:PHE506
|
4.0
|
28.4
|
1.0
|
C16
|
A:UKB601
|
4.0
|
26.4
|
1.0
|
CE1
|
A:PHE506
|
4.1
|
37.5
|
1.0
|
C
|
A:LEU505
|
4.2
|
31.3
|
1.0
|
C6
|
A:UKB601
|
4.2
|
25.9
|
1.0
|
C10
|
A:UKB601
|
4.3
|
28.7
|
1.0
|
OE1
|
A:GLN484
|
4.3
|
41.9
|
1.0
|
O
|
A:HOH705
|
4.4
|
47.9
|
1.0
|
O3
|
A:UKB601
|
4.4
|
27.9
|
1.0
|
CA
|
A:LEU505
|
4.4
|
28.1
|
1.0
|
CD2
|
A:PHE506
|
4.5
|
31.1
|
1.0
|
CD1
|
A:PHE506
|
4.6
|
35.3
|
1.0
|
C12
|
A:UKB601
|
4.7
|
33.5
|
1.0
|
CG
|
A:PHE506
|
4.8
|
32.4
|
1.0
|
CG
|
A:GLN484
|
4.8
|
37.8
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 7np5
Go back to
Fluorine Binding Sites List in 7np5
Fluorine binding site 2 out
of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
![](/pictures/F/pdb/np/7np5-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/np/7np5-F-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:38.7
occ:1.00
|
F2
|
A:UKB601
|
0.0
|
38.7
|
1.0
|
C15
|
A:UKB601
|
1.3
|
36.1
|
1.0
|
F1
|
A:UKB601
|
2.1
|
31.5
|
1.0
|
F3
|
A:UKB601
|
2.1
|
33.5
|
1.0
|
C14
|
A:UKB601
|
2.3
|
34.3
|
1.0
|
C13
|
A:UKB601
|
2.7
|
32.2
|
1.0
|
O
|
A:HOH705
|
3.3
|
47.9
|
1.0
|
OE1
|
A:GLN484
|
3.3
|
41.9
|
1.0
|
CD
|
A:GLN484
|
3.5
|
45.6
|
1.0
|
C9
|
A:UKB601
|
3.7
|
28.5
|
1.0
|
CE1
|
A:PHE506
|
3.7
|
37.5
|
1.0
|
CB
|
A:GLN487
|
3.7
|
36.4
|
1.0
|
NE2
|
A:GLN484
|
3.8
|
37.6
|
1.0
|
CG
|
A:GLN487
|
3.8
|
32.5
|
1.0
|
C12
|
A:UKB601
|
4.1
|
33.5
|
1.0
|
O
|
A:LEU505
|
4.1
|
33.7
|
1.0
|
CZ
|
A:PHE506
|
4.1
|
35.3
|
1.0
|
O
|
A:LEU483
|
4.1
|
33.8
|
1.0
|
CD1
|
A:PHE506
|
4.2
|
35.3
|
1.0
|
CA
|
A:GLN484
|
4.2
|
31.8
|
1.0
|
C8
|
A:UKB601
|
4.3
|
27.3
|
1.0
|
CG
|
A:GLN484
|
4.4
|
37.8
|
1.0
|
C
|
A:LEU483
|
4.4
|
31.1
|
1.0
|
N
|
A:GLN484
|
4.4
|
33.2
|
1.0
|
N1
|
A:UKB601
|
4.5
|
32.4
|
1.0
|
CD
|
A:GLN487
|
4.7
|
29.0
|
1.0
|
C10
|
A:UKB601
|
4.7
|
28.7
|
1.0
|
CE2
|
A:PHE506
|
4.8
|
28.4
|
1.0
|
CB
|
A:LEU483
|
4.8
|
30.6
|
1.0
|
CB
|
A:GLN484
|
4.9
|
31.6
|
1.0
|
C11
|
A:UKB601
|
4.9
|
33.9
|
1.0
|
CG
|
A:PHE506
|
4.9
|
32.4
|
1.0
|
O
|
A:HOH717
|
4.9
|
44.2
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 7np5
Go back to
Fluorine Binding Sites List in 7np5
Fluorine binding site 3 out
of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
![](/pictures/F/pdb/np/7np5-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/np/7np5-F-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:33.5
occ:1.00
|
F3
|
A:UKB601
|
0.0
|
33.5
|
1.0
|
C15
|
A:UKB601
|
1.3
|
36.1
|
1.0
|
F2
|
A:UKB601
|
2.1
|
38.7
|
1.0
|
F1
|
A:UKB601
|
2.1
|
31.5
|
1.0
|
C14
|
A:UKB601
|
2.4
|
34.3
|
1.0
|
N1
|
A:UKB601
|
2.9
|
32.4
|
1.0
|
C9
|
A:UKB601
|
3.2
|
28.5
|
1.0
|
C8
|
A:UKB601
|
3.3
|
27.3
|
1.0
|
C13
|
A:UKB601
|
3.3
|
32.2
|
1.0
|
CD
|
A:GLN484
|
3.3
|
45.6
|
1.0
|
NE2
|
A:GLN484
|
3.5
|
37.6
|
1.0
|
CB
|
A:LEU483
|
3.5
|
30.6
|
1.0
|
CG
|
A:GLN484
|
3.6
|
37.8
|
1.0
|
N
|
A:GLN484
|
3.7
|
33.2
|
1.0
|
C
|
A:LEU483
|
3.8
|
31.1
|
1.0
|
OE1
|
A:GLN484
|
3.8
|
41.9
|
1.0
|
CA
|
A:GLN484
|
4.0
|
31.8
|
1.0
|
O4
|
A:UKB601
|
4.0
|
30.6
|
1.0
|
O
|
A:VAL480
|
4.0
|
35.5
|
1.0
|
O
|
A:LEU483
|
4.1
|
33.8
|
1.0
|
CG1
|
A:VAL480
|
4.3
|
34.5
|
1.0
|
CA
|
A:LEU483
|
4.3
|
29.9
|
1.0
|
CB
|
A:GLN484
|
4.4
|
31.6
|
1.0
|
C10
|
A:UKB601
|
4.4
|
28.7
|
1.0
|
C7
|
A:UKB601
|
4.5
|
27.5
|
1.0
|
CD1
|
A:LEU483
|
4.5
|
33.3
|
1.0
|
C12
|
A:UKB601
|
4.5
|
33.5
|
1.0
|
CG
|
A:LEU483
|
4.7
|
30.7
|
1.0
|
CD1
|
A:LEU505
|
4.7
|
32.0
|
1.0
|
C16
|
A:UKB601
|
4.8
|
26.4
|
1.0
|
O
|
A:HOH705
|
4.8
|
47.9
|
1.0
|
C
|
A:VAL480
|
4.9
|
34.3
|
1.0
|
O
|
A:LEU505
|
4.9
|
33.7
|
1.0
|
C11
|
A:UKB601
|
5.0
|
33.9
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 7np5
Go back to
Fluorine Binding Sites List in 7np5
Fluorine binding site 4 out
of 4 in the Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216
![](/pictures/F/pdb/np/7np5-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/np/7np5-F-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Ror(Gamma)T Ligand Binding Domain in Complex with Allosteric Ligand FM216 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:32.7
occ:1.00
|
F4
|
A:UKB601
|
0.0
|
32.7
|
1.0
|
C22
|
A:UKB601
|
1.3
|
30.6
|
1.0
|
C21
|
A:UKB601
|
2.3
|
30.0
|
1.0
|
C2
|
A:UKB601
|
2.4
|
26.8
|
1.0
|
O1
|
A:UKB601
|
2.6
|
32.4
|
1.0
|
C1
|
A:UKB601
|
2.9
|
27.8
|
1.0
|
CG2
|
A:THR325
|
3.0
|
28.4
|
0.5
|
NE2
|
A:GLN329
|
3.1
|
31.2
|
1.0
|
CG
|
A:GLN329
|
3.4
|
27.8
|
1.0
|
CD
|
A:GLN329
|
3.5
|
35.3
|
1.0
|
C5
|
A:UKB601
|
3.6
|
26.1
|
1.0
|
C3
|
A:UKB601
|
3.6
|
29.3
|
1.0
|
CG1
|
A:VAL494
|
3.7
|
34.0
|
1.0
|
O
|
A:THR325
|
3.9
|
29.1
|
0.5
|
CB
|
A:THR325
|
3.9
|
32.9
|
0.5
|
O
|
A:THR325
|
3.9
|
29.3
|
0.5
|
O2
|
A:UKB601
|
4.1
|
31.5
|
1.0
|
C4
|
A:UKB601
|
4.1
|
28.9
|
1.0
|
CB
|
A:THR325
|
4.2
|
33.7
|
0.5
|
CA
|
A:THR325
|
4.4
|
28.5
|
0.5
|
C
|
A:THR325
|
4.4
|
33.3
|
0.5
|
C
|
A:THR325
|
4.5
|
33.2
|
0.5
|
CA
|
A:THR325
|
4.5
|
28.4
|
0.5
|
CG2
|
A:THR325
|
4.5
|
34.8
|
0.5
|
OE1
|
A:GLN329
|
4.5
|
35.5
|
1.0
|
OG1
|
A:THR325
|
4.7
|
35.5
|
0.5
|
O
|
A:GLN495
|
4.8
|
39.0
|
1.0
|
O3
|
A:UKB601
|
4.8
|
27.9
|
1.0
|
CB
|
A:GLN329
|
4.8
|
27.0
|
1.0
|
OG1
|
A:THR325
|
4.9
|
28.2
|
0.5
|
CG2
|
A:ILE328
|
4.9
|
28.0
|
1.0
|
C6
|
A:UKB601
|
5.0
|
25.9
|
1.0
|
|
Reference:
F.A.Meijer,
A.O.W.M.Saris,
R.G.Doveston,
G.J.M.Oerlemans,
R.M.J.M.De Vries,
B.A.Somsen,
A.Unger,
B.Klebl,
C.Ottmann,
P.J.Cossar,
L.Brunsveld.
Structure-Activity Relationship Studies of Trisubstituted Isoxazoles As Selective Allosteric Ligands For the Retinoic-Acid-Receptor-Related Orphan Receptor Gamma T. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34008974
DOI: 10.1021/ACS.JMEDCHEM.1C00475
Page generated: Fri Aug 2 10:12:15 2024
|