Fluorine in PDB 6yjm: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm
was solved by
A.Goepfert,
P.Leonard,
N.Triballeau,
D.Fleury,
P.Mollat,
M.Lamers,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
18.47 /
2.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.32,
80.24,
51.05,
90,
90.2,
90
|
R / Rfree (%)
|
21.3 /
25.6
|
Other elements in 6yjm:
The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
(pdb code 6yjm). 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 Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972, PDB code: 6yjm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6yjm
Go back to
Fluorine Binding Sites List in 6yjm
Fluorine binding site 1 out
of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
![](/pictures/F/pdb/yj/6yjm-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/yj/6yjm-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 Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F505
b:14.5
occ:1.00
|
F28
|
A:OU5505
|
0.0
|
14.5
|
1.0
|
C26
|
A:OU5505
|
1.3
|
17.1
|
1.0
|
C25
|
A:OU5505
|
2.4
|
14.5
|
1.0
|
C27
|
A:OU5505
|
2.4
|
13.6
|
1.0
|
O
|
A:ARG437
|
3.2
|
13.2
|
1.0
|
CG2
|
A:THR444
|
3.4
|
21.6
|
1.0
|
CD1
|
A:ILE446
|
3.5
|
22.9
|
1.0
|
O
|
A:LEU438
|
3.6
|
12.5
|
1.0
|
C24
|
A:OU5505
|
3.6
|
14.1
|
1.0
|
C22
|
A:OU5505
|
3.6
|
15.5
|
1.0
|
CB
|
A:SER440
|
3.9
|
17.8
|
1.0
|
O
|
A:ILE442
|
3.9
|
16.3
|
1.0
|
C
|
A:LEU438
|
4.0
|
14.3
|
1.0
|
CA
|
A:LEU438
|
4.1
|
17.3
|
1.0
|
C23
|
A:OU5505
|
4.1
|
11.3
|
1.0
|
O
|
A:THR444
|
4.2
|
31.3
|
1.0
|
C
|
A:ARG437
|
4.2
|
16.2
|
1.0
|
N
|
A:SER440
|
4.3
|
14.3
|
1.0
|
O
|
A:SER440
|
4.3
|
22.5
|
1.0
|
N
|
A:THR444
|
4.4
|
24.1
|
1.0
|
CG1
|
A:ILE446
|
4.5
|
24.3
|
1.0
|
CA
|
A:SER440
|
4.5
|
15.7
|
1.0
|
OG
|
A:SER440
|
4.6
|
20.4
|
1.0
|
N
|
A:LEU438
|
4.7
|
15.6
|
1.0
|
CB
|
A:THR444
|
4.7
|
25.4
|
1.0
|
F29
|
A:OU5505
|
4.7
|
18.1
|
1.0
|
N18
|
A:OU5505
|
4.8
|
15.9
|
1.0
|
C
|
A:SER440
|
4.8
|
19.7
|
1.0
|
C
|
A:THR444
|
4.9
|
29.6
|
1.0
|
CA
|
A:THR444
|
4.9
|
26.2
|
1.0
|
N
|
A:MET439
|
4.9
|
9.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6yjm
Go back to
Fluorine Binding Sites List in 6yjm
Fluorine binding site 2 out
of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
![](/pictures/F/pdb/yj/6yjm-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/yj/6yjm-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 Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F505
b:18.1
occ:1.00
|
F29
|
A:OU5505
|
0.0
|
18.1
|
1.0
|
C24
|
A:OU5505
|
1.3
|
14.1
|
1.0
|
C25
|
A:OU5505
|
2.4
|
14.5
|
1.0
|
C23
|
A:OU5505
|
2.4
|
11.3
|
1.0
|
CB
|
A:PHE406
|
3.2
|
10.2
|
1.0
|
CB
|
A:HIS403
|
3.3
|
15.2
|
1.0
|
ND1
|
A:HIS403
|
3.3
|
17.2
|
1.0
|
CG
|
A:HIS403
|
3.5
|
20.5
|
1.0
|
C26
|
A:OU5505
|
3.6
|
17.1
|
1.0
|
C22
|
A:OU5505
|
3.6
|
15.5
|
1.0
|
CD2
|
A:PHE406
|
3.7
|
27.8
|
1.0
|
CD2
|
A:LEU443
|
3.8
|
17.6
|
1.0
|
CG
|
A:PHE406
|
3.9
|
18.1
|
1.0
|
O
|
A:HIS403
|
4.0
|
15.4
|
1.0
|
CA
|
A:HIS403
|
4.1
|
14.8
|
1.0
|
C27
|
A:OU5505
|
4.1
|
13.6
|
1.0
|
CE1
|
A:HIS403
|
4.3
|
20.7
|
1.0
|
OG1
|
A:THR407
|
4.4
|
17.4
|
1.0
|
CA
|
A:PHE406
|
4.4
|
11.0
|
1.0
|
N
|
A:THR407
|
4.5
|
12.8
|
1.0
|
C
|
A:HIS403
|
4.5
|
13.3
|
1.0
|
C
|
A:PHE406
|
4.5
|
17.2
|
1.0
|
CD2
|
A:HIS403
|
4.6
|
18.5
|
1.0
|
F28
|
A:OU5505
|
4.7
|
14.5
|
1.0
|
N18
|
A:OU5505
|
4.8
|
15.9
|
1.0
|
C17
|
A:OU5505
|
4.9
|
16.4
|
1.0
|
CE2
|
A:PHE406
|
4.9
|
24.6
|
1.0
|
NE2
|
A:HIS403
|
5.0
|
16.4
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6yjm
Go back to
Fluorine Binding Sites List in 6yjm
Fluorine binding site 3 out
of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
![](/pictures/F/pdb/yj/6yjm-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/yj/6yjm-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 Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F505
b:18.3
occ:1.00
|
F28
|
B:OU5505
|
0.0
|
18.3
|
1.0
|
C26
|
B:OU5505
|
1.3
|
18.9
|
1.0
|
C27
|
B:OU5505
|
2.4
|
18.5
|
1.0
|
C25
|
B:OU5505
|
2.4
|
18.1
|
1.0
|
O
|
B:ARG437
|
3.3
|
17.7
|
1.0
|
CG2
|
B:THR444
|
3.4
|
23.8
|
1.0
|
CD1
|
B:ILE446
|
3.5
|
24.2
|
1.0
|
C24
|
B:OU5505
|
3.6
|
20.9
|
1.0
|
C22
|
B:OU5505
|
3.6
|
16.0
|
1.0
|
O
|
B:LEU438
|
3.7
|
17.1
|
1.0
|
O
|
B:ILE442
|
3.8
|
19.2
|
1.0
|
CB
|
B:SER440
|
3.9
|
16.3
|
1.0
|
O
|
B:THR444
|
4.0
|
33.9
|
1.0
|
C
|
B:LEU438
|
4.1
|
18.5
|
1.0
|
C23
|
B:OU5505
|
4.1
|
18.3
|
1.0
|
CA
|
B:LEU438
|
4.1
|
19.5
|
1.0
|
N
|
B:THR444
|
4.2
|
23.5
|
1.0
|
O
|
B:SER440
|
4.3
|
18.6
|
1.0
|
C
|
B:ARG437
|
4.3
|
22.5
|
1.0
|
N
|
B:SER440
|
4.4
|
17.7
|
1.0
|
CG1
|
B:ILE446
|
4.4
|
26.6
|
1.0
|
OG
|
B:SER440
|
4.5
|
22.0
|
1.0
|
CA
|
B:SER440
|
4.6
|
17.0
|
1.0
|
CB
|
B:THR444
|
4.7
|
22.7
|
1.0
|
N
|
B:LEU438
|
4.7
|
14.2
|
1.0
|
F29
|
B:OU5505
|
4.7
|
14.3
|
1.0
|
C
|
B:THR444
|
4.8
|
23.7
|
1.0
|
N18
|
B:OU5505
|
4.8
|
16.0
|
1.0
|
CA
|
B:THR444
|
4.8
|
21.7
|
1.0
|
C
|
B:SER440
|
4.8
|
19.9
|
1.0
|
CA
|
B:LEU443
|
4.9
|
19.4
|
1.0
|
C
|
B:ILE442
|
4.9
|
20.0
|
1.0
|
C
|
B:LEU443
|
4.9
|
18.3
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6yjm
Go back to
Fluorine Binding Sites List in 6yjm
Fluorine binding site 4 out
of 4 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972
![](/pictures/F/pdb/yj/6yjm-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/yj/6yjm-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 Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F505
b:14.3
occ:1.00
|
F29
|
B:OU5505
|
0.0
|
14.3
|
1.0
|
C24
|
B:OU5505
|
1.3
|
20.9
|
1.0
|
C23
|
B:OU5505
|
2.4
|
18.3
|
1.0
|
C25
|
B:OU5505
|
2.4
|
18.1
|
1.0
|
CB
|
B:PHE406
|
3.1
|
18.3
|
1.0
|
CB
|
B:HIS403
|
3.3
|
16.0
|
1.0
|
CD2
|
B:PHE406
|
3.5
|
29.3
|
1.0
|
CD2
|
B:HIS403
|
3.5
|
20.2
|
1.0
|
CG
|
B:HIS403
|
3.5
|
21.2
|
1.0
|
C26
|
B:OU5505
|
3.6
|
18.9
|
1.0
|
C22
|
B:OU5505
|
3.6
|
16.0
|
1.0
|
CD2
|
B:LEU443
|
3.7
|
22.0
|
1.0
|
CG
|
B:PHE406
|
3.7
|
22.3
|
1.0
|
O
|
B:HIS403
|
4.0
|
19.0
|
1.0
|
CA
|
B:HIS403
|
4.1
|
18.7
|
1.0
|
C27
|
B:OU5505
|
4.1
|
18.5
|
1.0
|
CA
|
B:PHE406
|
4.4
|
15.6
|
1.0
|
OG1
|
B:THR407
|
4.4
|
12.6
|
1.0
|
N
|
B:THR407
|
4.5
|
13.3
|
1.0
|
C
|
B:PHE406
|
4.5
|
15.1
|
1.0
|
NE2
|
B:HIS403
|
4.5
|
20.5
|
1.0
|
C
|
B:HIS403
|
4.6
|
17.3
|
1.0
|
ND1
|
B:HIS403
|
4.6
|
22.1
|
1.0
|
CE2
|
B:PHE406
|
4.7
|
37.3
|
1.0
|
F28
|
B:OU5505
|
4.7
|
18.3
|
1.0
|
N18
|
B:OU5505
|
4.8
|
16.0
|
1.0
|
C17
|
B:OU5505
|
4.8
|
12.8
|
1.0
|
CD1
|
B:LEU379
|
4.9
|
13.0
|
1.0
|
|
Reference:
P.Leonard,
N.Triballeau,
P.Mollat.
Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with the Inhibitor GLPG1972 To Be Published.
Page generated: Fri Aug 2 04:42:19 2024
|