Fluorine in PDB 7zqx: Human Galectin-3C in Complex with A Galactose Derivative
Protein crystallography data
The structure of Human Galectin-3C in Complex with A Galactose Derivative, PDB code: 7zqx
was solved by
F.Zetterberg,
U.J.Nilsson,
M.Hakansson,
D.T.Logan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.06 /
1.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.404,
58.088,
62.575,
90,
90,
90
|
R / Rfree (%)
|
10.9 /
12.9
|
Other elements in 7zqx:
The structure of Human Galectin-3C in Complex with A Galactose Derivative also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Human Galectin-3C in Complex with A Galactose Derivative
(pdb code 7zqx). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Human Galectin-3C in Complex with A Galactose Derivative, PDB code: 7zqx:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7zqx
Go back to
Fluorine Binding Sites List in 7zqx
Fluorine binding site 1 out
of 3 in the Human Galectin-3C in Complex with A Galactose Derivative
![](/pictures/F/pdb/zq/7zqx-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/zq/7zqx-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 Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2406
b:11.5
occ:1.00
|
F2
|
A:JU02406
|
0.0
|
11.5
|
1.0
|
C12
|
A:JU02406
|
1.4
|
10.1
|
1.0
|
C11
|
A:JU02406
|
2.3
|
11.5
|
1.0
|
C13
|
A:JU02406
|
2.4
|
9.4
|
1.0
|
F1
|
A:JU02406
|
2.7
|
13.8
|
1.0
|
C
|
A:ILE145
|
3.0
|
7.3
|
1.0
|
CG
|
A:ARG144
|
3.3
|
11.2
|
1.0
|
O
|
A:ILE145
|
3.3
|
7.6
|
1.0
|
N
|
A:ALA146
|
3.3
|
7.7
|
1.0
|
N
|
A:ILE145
|
3.3
|
8.0
|
1.0
|
CB
|
A:ARG144
|
3.4
|
10.2
|
1.0
|
CB
|
A:ALA146
|
3.5
|
8.8
|
1.0
|
CA
|
A:ILE145
|
3.5
|
8.1
|
1.0
|
CD
|
A:ARG144
|
3.6
|
12.4
|
1.0
|
C10
|
A:JU02406
|
3.6
|
13.2
|
1.0
|
C
|
A:ARG144
|
3.6
|
8.4
|
1.0
|
C8
|
A:JU02406
|
3.6
|
10.5
|
1.0
|
ND2
|
A:ASN160
|
3.6
|
9.2
|
1.0
|
CA
|
A:ALA146
|
3.9
|
7.8
|
1.0
|
O
|
A:ARG144
|
4.1
|
9.3
|
1.0
|
NE
|
A:ARG144
|
4.1
|
14.0
|
1.0
|
C9
|
A:JU02406
|
4.1
|
13.3
|
1.0
|
CA
|
A:ARG144
|
4.1
|
8.8
|
1.0
|
O
|
A:SER237
|
4.4
|
8.6
|
0.8
|
CA
|
A:GLY238
|
4.5
|
8.8
|
1.0
|
O
|
A:SER237
|
4.5
|
8.1
|
0.2
|
OG
|
A:SER237
|
4.5
|
9.8
|
0.8
|
F
|
A:JU02406
|
4.6
|
17.0
|
1.0
|
CZ
|
A:ARG144
|
4.7
|
16.0
|
1.0
|
C
|
A:SER237
|
4.7
|
8.1
|
0.2
|
S
|
A:SCN2402
|
4.7
|
18.9
|
1.0
|
C
|
A:SER237
|
4.8
|
8.1
|
0.8
|
CG
|
A:ASN160
|
4.8
|
8.2
|
1.0
|
C7
|
A:JU02406
|
4.8
|
10.7
|
1.0
|
N
|
A:GLY238
|
4.8
|
8.7
|
1.0
|
C
|
A:SCN2402
|
4.9
|
19.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7zqx
Go back to
Fluorine Binding Sites List in 7zqx
Fluorine binding site 2 out
of 3 in the Human Galectin-3C in Complex with A Galactose Derivative
![](/pictures/F/pdb/zq/7zqx-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/zq/7zqx-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 Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2406
b:13.8
occ:1.00
|
F1
|
A:JU02406
|
0.0
|
13.8
|
1.0
|
C11
|
A:JU02406
|
1.4
|
11.5
|
1.0
|
C10
|
A:JU02406
|
2.4
|
13.2
|
1.0
|
C12
|
A:JU02406
|
2.4
|
10.1
|
1.0
|
F
|
A:JU02406
|
2.7
|
17.0
|
1.0
|
F2
|
A:JU02406
|
2.7
|
11.5
|
1.0
|
N
|
A:GLY238
|
3.0
|
8.7
|
1.0
|
CA
|
A:GLY238
|
3.0
|
8.8
|
1.0
|
OG
|
A:SER237
|
3.3
|
9.8
|
0.8
|
C
|
A:SER237
|
3.4
|
8.1
|
0.2
|
CB
|
A:SER237
|
3.4
|
9.0
|
0.2
|
C
|
A:SER237
|
3.4
|
8.1
|
0.8
|
O
|
A:HOH2605
|
3.5
|
26.4
|
1.0
|
NE
|
A:ARG144
|
3.5
|
14.0
|
1.0
|
CB
|
A:SER237
|
3.6
|
9.7
|
0.8
|
C13
|
A:JU02406
|
3.6
|
9.4
|
1.0
|
C9
|
A:JU02406
|
3.6
|
13.3
|
1.0
|
O
|
A:SER237
|
3.8
|
8.6
|
0.8
|
CZ
|
A:ARG144
|
3.8
|
16.0
|
1.0
|
O
|
A:SER237
|
3.9
|
8.1
|
0.2
|
NH2
|
A:ARG144
|
3.9
|
20.6
|
1.0
|
CA
|
A:SER237
|
4.0
|
8.3
|
0.2
|
CG
|
A:ARG144
|
4.0
|
11.2
|
1.0
|
CD
|
A:ARG144
|
4.1
|
12.4
|
1.0
|
CA
|
A:SER237
|
4.1
|
8.2
|
0.8
|
C8
|
A:JU02406
|
4.1
|
10.5
|
1.0
|
O
|
A:HOH2674
|
4.2
|
12.2
|
1.0
|
O
|
A:HOH2529
|
4.5
|
24.9
|
1.0
|
C
|
A:GLY238
|
4.5
|
8.4
|
1.0
|
N
|
A:ALA146
|
4.5
|
7.7
|
1.0
|
O
|
A:HOH2606
|
4.5
|
17.0
|
1.0
|
OG
|
A:SER237
|
4.6
|
11.0
|
0.2
|
NH1
|
A:ARG144
|
4.6
|
18.9
|
1.0
|
CB
|
A:ALA146
|
4.6
|
8.8
|
1.0
|
O
|
A:ARG144
|
4.7
|
9.3
|
1.0
|
C
|
A:ILE145
|
4.8
|
7.3
|
1.0
|
CA
|
A:ILE145
|
4.9
|
8.1
|
1.0
|
O
|
A:HOH2727
|
4.9
|
27.4
|
1.0
|
C
|
A:ARG144
|
5.0
|
8.4
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7zqx
Go back to
Fluorine Binding Sites List in 7zqx
Fluorine binding site 3 out
of 3 in the Human Galectin-3C in Complex with A Galactose Derivative
![](/pictures/F/pdb/zq/7zqx-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/zq/7zqx-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 Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2406
b:17.0
occ:1.00
|
F
|
A:JU02406
|
0.0
|
17.0
|
1.0
|
C10
|
A:JU02406
|
1.3
|
13.2
|
1.0
|
C11
|
A:JU02406
|
2.3
|
11.5
|
1.0
|
C9
|
A:JU02406
|
2.4
|
13.3
|
1.0
|
F1
|
A:JU02406
|
2.7
|
13.8
|
1.0
|
O
|
A:HOH2606
|
3.1
|
17.0
|
1.0
|
NH2
|
A:ARG144
|
3.3
|
20.6
|
1.0
|
O
|
A:HOH2727
|
3.3
|
27.4
|
1.0
|
C12
|
A:JU02406
|
3.5
|
10.1
|
1.0
|
C8
|
A:JU02406
|
3.6
|
10.5
|
1.0
|
OG
|
A:SER237
|
3.6
|
9.8
|
0.8
|
CZ
|
A:ARG144
|
3.7
|
16.0
|
1.0
|
CB
|
A:SER237
|
3.8
|
9.0
|
0.2
|
O
|
A:HOH2605
|
3.9
|
26.4
|
1.0
|
CB
|
A:SER237
|
3.9
|
9.7
|
0.8
|
O
|
A:HOH2561
|
4.0
|
34.3
|
1.0
|
C13
|
A:JU02406
|
4.1
|
9.4
|
1.0
|
NH1
|
A:ARG144
|
4.1
|
18.9
|
1.0
|
OG
|
A:SER237
|
4.3
|
11.0
|
0.2
|
O
|
A:HOH2638
|
4.3
|
40.4
|
1.0
|
NE
|
A:ARG144
|
4.3
|
14.0
|
1.0
|
O
|
A:HOH2674
|
4.3
|
12.2
|
1.0
|
F2
|
A:JU02406
|
4.6
|
11.5
|
1.0
|
C7
|
A:JU02406
|
4.8
|
10.7
|
1.0
|
N
|
A:GLY238
|
4.9
|
8.7
|
1.0
|
|
Reference:
F.R.Zetterberg,
A.Mackinnon,
T.Brimert,
L.Gravelle,
R.E.Johnsson,
B.Kahl-Knutson,
H.Leffler,
U.J.Nilsson,
A.Pedersen,
K.Peterson,
J.A.Roper,
H.Schambye,
R.J.Slack,
S.Tantawi.
Discovery and Optimization of the First Highly Effective and Orally Available Galectin-3 Inhibitors For Treatment of Fibrotic Disease. J.Med.Chem. V. 65 12626 2022.
ISSN: ISSN 0022-2623
PubMed: 36154172
DOI: 10.1021/ACS.JMEDCHEM.2C00660
Page generated: Fri Aug 2 16:18:36 2024
|