Fluorine in PDB 7df5: Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor
Protein crystallography data
The structure of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df5
was solved by
K.Ghosh,
A.Kumar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.30 /
1.08
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.21,
57.34,
62.06,
90,
90,
90
|
R / Rfree (%)
|
13.9 /
16.9
|
Other elements in 7df5:
The structure of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor
(pdb code 7df5). 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-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df5:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7df5
Go back to
Fluorine Binding Sites List in 7df5
Fluorine binding site 1 out
of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F306
b:14.6
occ:1.00
|
F2
|
A:H5O306
|
0.0
|
14.6
|
1.0
|
C13
|
A:H5O306
|
1.3
|
13.6
|
1.0
|
C12
|
A:H5O306
|
2.3
|
15.8
|
1.0
|
C14
|
A:H5O306
|
2.4
|
13.2
|
1.0
|
H17
|
A:H5O306
|
2.6
|
13.7
|
1.0
|
F1
|
A:H5O306
|
2.6
|
18.1
|
1.0
|
HG3
|
A:ARG144
|
2.6
|
15.3
|
1.0
|
HB2
|
A:ARG144
|
2.7
|
14.2
|
1.0
|
HB2
|
A:ALA146
|
2.8
|
11.4
|
1.0
|
C
|
A:ILE145
|
3.0
|
10.8
|
1.0
|
HD2
|
A:ARG144
|
3.2
|
16.8
|
1.0
|
O
|
A:ILE145
|
3.3
|
10.9
|
1.0
|
CG
|
A:ARG144
|
3.3
|
15.4
|
1.0
|
HD22
|
A:ASN160
|
3.3
|
11.9
|
0.0
|
N
|
A:ILE145
|
3.3
|
11.1
|
1.0
|
N
|
A:ALA146
|
3.3
|
10.5
|
1.0
|
CB
|
A:ARG144
|
3.4
|
14.5
|
1.0
|
HD21
|
A:ASN160
|
3.4
|
11.9
|
0.0
|
HA
|
A:ILE145
|
3.4
|
11.0
|
1.0
|
HB3
|
A:ALA146
|
3.4
|
11.7
|
1.0
|
CA
|
A:ILE145
|
3.5
|
10.7
|
1.0
|
CB
|
A:ALA146
|
3.5
|
11.8
|
1.0
|
H
|
A:ILE145
|
3.5
|
11.2
|
1.0
|
C11
|
A:H5O306
|
3.5
|
18.3
|
1.0
|
ND2
|
A:ASN160
|
3.6
|
12.0
|
1.0
|
C
|
A:ARG144
|
3.6
|
12.6
|
1.0
|
C9
|
A:H5O306
|
3.6
|
14.7
|
1.0
|
H
|
A:ALA146
|
3.6
|
10.4
|
1.0
|
CD
|
A:ARG144
|
3.7
|
15.9
|
1.0
|
HA3
|
A:GLY238
|
3.7
|
12.3
|
1.0
|
CA
|
A:ALA146
|
3.9
|
10.0
|
1.0
|
O
|
A:ARG144
|
4.1
|
12.8
|
1.0
|
CA
|
A:ARG144
|
4.1
|
12.3
|
1.0
|
C10
|
A:H5O306
|
4.1
|
17.2
|
1.0
|
NE
|
A:ARG144
|
4.1
|
20.7
|
1.0
|
HG2
|
A:ARG144
|
4.1
|
15.3
|
1.0
|
HB3
|
A:ARG144
|
4.2
|
13.9
|
1.0
|
HA2
|
A:GLY238
|
4.3
|
12.3
|
1.0
|
HA
|
A:ALA146
|
4.3
|
10.1
|
1.0
|
HE
|
A:ARG144
|
4.3
|
20.7
|
1.0
|
HB1
|
A:ALA146
|
4.3
|
11.4
|
1.0
|
CA
|
A:GLY238
|
4.4
|
12.1
|
1.0
|
O
|
A:SER237
|
4.4
|
11.7
|
1.0
|
HA
|
A:ARG144
|
4.5
|
12.4
|
1.0
|
OG
|
A:SER237
|
4.5
|
15.3
|
1.0
|
HD3
|
A:ARG144
|
4.5
|
16.5
|
1.0
|
F
|
A:H5O306
|
4.6
|
23.2
|
1.0
|
HH21
|
A:ARG144
|
4.7
|
27.7
|
1.0
|
CZ
|
A:ARG144
|
4.7
|
26.1
|
1.0
|
HG
|
A:SER237
|
4.7
|
15.2
|
0.0
|
CG
|
A:ASN160
|
4.8
|
11.0
|
1.0
|
C
|
A:SER237
|
4.8
|
11.6
|
1.0
|
C8
|
A:H5O306
|
4.8
|
14.7
|
1.0
|
CL
|
A:CL302
|
4.9
|
18.3
|
1.0
|
N
|
A:GLY238
|
4.9
|
12.2
|
1.0
|
NH2
|
A:ARG144
|
4.9
|
28.9
|
1.0
|
H15
|
A:H5O306
|
4.9
|
13.6
|
1.0
|
CB
|
A:ILE145
|
5.0
|
12.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7df5
Go back to
Fluorine Binding Sites List in 7df5
Fluorine binding site 2 out
of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F306
b:18.1
occ:1.00
|
F1
|
A:H5O306
|
0.0
|
18.1
|
1.0
|
C12
|
A:H5O306
|
1.3
|
15.8
|
1.0
|
C13
|
A:H5O306
|
2.3
|
13.6
|
1.0
|
C11
|
A:H5O306
|
2.3
|
18.3
|
1.0
|
HA2
|
A:GLY238
|
2.6
|
12.3
|
1.0
|
F2
|
A:H5O306
|
2.6
|
14.6
|
1.0
|
F
|
A:H5O306
|
2.7
|
23.2
|
1.0
|
HA3
|
A:GLY238
|
2.9
|
12.3
|
1.0
|
CA
|
A:GLY238
|
3.0
|
12.1
|
1.0
|
N
|
A:GLY238
|
3.1
|
12.2
|
1.0
|
HB2
|
A:SER237
|
3.1
|
14.2
|
1.0
|
HG3
|
A:ARG144
|
3.1
|
15.3
|
1.0
|
OG
|
A:SER237
|
3.2
|
15.3
|
1.0
|
HG
|
A:SER237
|
3.3
|
15.2
|
0.0
|
C
|
A:SER237
|
3.4
|
11.6
|
1.0
|
HE
|
A:ARG144
|
3.4
|
20.7
|
1.0
|
H
|
A:GLY238
|
3.4
|
12.0
|
1.0
|
CB
|
A:SER237
|
3.6
|
14.5
|
1.0
|
NE
|
A:ARG144
|
3.6
|
20.7
|
1.0
|
C14
|
A:H5O306
|
3.6
|
13.2
|
1.0
|
C10
|
A:H5O306
|
3.6
|
17.2
|
1.0
|
O
|
A:SER237
|
3.8
|
11.7
|
1.0
|
CZ
|
A:ARG144
|
3.8
|
26.1
|
1.0
|
HH11
|
A:ARG144
|
3.9
|
30.3
|
1.0
|
HB3
|
A:ALA146
|
3.9
|
11.7
|
1.0
|
CG
|
A:ARG144
|
4.0
|
15.4
|
1.0
|
HD2
|
A:ARG144
|
4.0
|
16.8
|
1.0
|
NH1
|
A:ARG144
|
4.0
|
32.0
|
1.0
|
CD
|
A:ARG144
|
4.1
|
15.9
|
1.0
|
CA
|
A:SER237
|
4.1
|
12.3
|
1.0
|
C9
|
A:H5O306
|
4.1
|
14.7
|
1.0
|
H
|
A:ALA146
|
4.2
|
10.4
|
1.0
|
HA
|
A:ILE145
|
4.2
|
11.0
|
1.0
|
O
|
A:HOH524
|
4.3
|
17.5
|
1.0
|
O
|
A:HOH505
|
4.3
|
31.1
|
1.0
|
HB2
|
A:ALA146
|
4.3
|
11.4
|
1.0
|
H17
|
A:H5O306
|
4.4
|
13.7
|
1.0
|
N
|
A:ALA146
|
4.4
|
10.5
|
1.0
|
O
|
A:HOH464
|
4.4
|
25.3
|
1.0
|
HB3
|
A:SER237
|
4.4
|
14.2
|
1.0
|
C
|
A:GLY238
|
4.5
|
12.1
|
1.0
|
HG2
|
A:ARG144
|
4.5
|
15.3
|
1.0
|
H16
|
A:H5O306
|
4.5
|
16.7
|
1.0
|
HH12
|
A:ARG144
|
4.5
|
29.7
|
1.0
|
CB
|
A:ALA146
|
4.6
|
11.8
|
1.0
|
NH2
|
A:ARG144
|
4.6
|
28.9
|
1.0
|
O
|
A:HOH488
|
4.6
|
23.6
|
1.0
|
O
|
A:ARG144
|
4.6
|
12.8
|
1.0
|
HB2
|
A:ARG144
|
4.7
|
14.2
|
1.0
|
HA
|
A:SER237
|
4.7
|
12.3
|
1.0
|
C
|
A:ILE145
|
4.7
|
10.8
|
1.0
|
CA
|
A:ILE145
|
4.8
|
10.7
|
1.0
|
HH21
|
A:ARG144
|
4.8
|
27.7
|
1.0
|
C
|
A:ARG144
|
4.9
|
12.6
|
1.0
|
CB
|
A:ARG144
|
4.9
|
14.5
|
1.0
|
H
|
A:ASP239
|
4.9
|
11.9
|
1.0
|
N
|
A:ILE145
|
5.0
|
11.1
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7df5
Go back to
Fluorine Binding Sites List in 7df5
Fluorine binding site 3 out
of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F306
b:23.2
occ:1.00
|
F
|
A:H5O306
|
0.0
|
23.2
|
1.0
|
C11
|
A:H5O306
|
1.3
|
18.3
|
1.0
|
C12
|
A:H5O306
|
2.3
|
15.8
|
1.0
|
C10
|
A:H5O306
|
2.4
|
17.2
|
1.0
|
H16
|
A:H5O306
|
2.6
|
16.7
|
1.0
|
F1
|
A:H5O306
|
2.7
|
18.1
|
1.0
|
HG
|
A:SER237
|
3.0
|
15.2
|
0.0
|
O
|
A:HOH488
|
3.0
|
23.6
|
1.0
|
HB2
|
A:SER237
|
3.1
|
14.2
|
1.0
|
HH12
|
A:ARG144
|
3.4
|
29.7
|
1.0
|
NH1
|
A:ARG144
|
3.4
|
32.0
|
1.0
|
OG
|
A:SER237
|
3.5
|
15.3
|
1.0
|
HH11
|
A:ARG144
|
3.5
|
30.3
|
1.0
|
C13
|
A:H5O306
|
3.5
|
13.6
|
1.0
|
C9
|
A:H5O306
|
3.6
|
14.7
|
1.0
|
CZ
|
A:ARG144
|
3.8
|
26.1
|
1.0
|
CB
|
A:SER237
|
3.8
|
14.5
|
1.0
|
O
|
A:HOH471
|
3.8
|
45.2
|
1.0
|
C14
|
A:H5O306
|
4.0
|
13.2
|
1.0
|
HH22
|
A:ARG144
|
4.1
|
27.7
|
1.0
|
NH2
|
A:ARG144
|
4.1
|
28.9
|
1.0
|
HB3
|
A:SER237
|
4.2
|
14.2
|
1.0
|
NE
|
A:ARG144
|
4.4
|
20.7
|
1.0
|
O
|
A:HOH505
|
4.4
|
31.1
|
1.0
|
O
|
A:HOH524
|
4.4
|
17.5
|
1.0
|
HE
|
A:ARG144
|
4.5
|
20.7
|
1.0
|
F2
|
A:H5O306
|
4.6
|
14.6
|
1.0
|
HH21
|
A:ARG144
|
4.7
|
27.7
|
1.0
|
HA2
|
A:GLY238
|
4.7
|
12.3
|
1.0
|
H
|
A:GLY238
|
4.7
|
12.0
|
1.0
|
C8
|
A:H5O306
|
4.8
|
14.7
|
1.0
|
N
|
A:GLY238
|
4.8
|
12.2
|
1.0
|
HB3
|
A:ALA146
|
4.8
|
11.7
|
1.0
|
O
|
A:HOH440
|
4.9
|
18.0
|
1.0
|
|
Reference:
L.Xu,
R.A.Hartz,
B.R.Beno,
K.Ghosh,
J.K.Shukla,
A.Kumar,
D.Patel,
N.Kalidindi,
N.Lemos,
S.S.Gautam,
A.Kumar,
B.A.Ellsworth,
D.Shah,
H.Sale,
D.Cheng,
A.Regueiro-Ren.
Synthesis, Structure-Activity Relationships, and in Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics As Galectin-3 Inhibitors. J.Med.Chem. V. 64 6634 2021.
ISSN: ISSN 0022-2623
PubMed: 33988358
DOI: 10.1021/ACS.JMEDCHEM.0C02001
Page generated: Fri Aug 2 06:27:00 2024
|