Fluorine in PDB 6gou: Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Enzymatic activity of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
All present enzymatic activity of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I:
2.5.1.26;
Protein crystallography data
The structure of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I, PDB code: 6gou
was solved by
A.Mattevi,
V.Piano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.00 /
2.90
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
147.958,
120.644,
148.160,
90.00,
95.27,
90.00
|
R / Rfree (%)
|
21.9 /
25.8
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
(pdb code 6gou). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I, PDB code: 6gou:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 1 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F702
b:47.6
occ:1.00
|
FAT
|
D:F6T702
|
0.0
|
47.6
|
1.0
|
CAS
|
D:F6T702
|
1.3
|
44.6
|
1.0
|
CAU
|
D:F6T702
|
2.3
|
44.5
|
1.0
|
CAR
|
D:F6T702
|
2.4
|
43.0
|
1.0
|
CAB
|
D:F6T702
|
2.8
|
43.4
|
1.0
|
N
|
D:ARG515
|
2.9
|
30.6
|
1.0
|
CA
|
D:ARG515
|
2.9
|
35.0
|
1.0
|
CAC
|
D:F6T702
|
3.0
|
40.7
|
1.0
|
CAA
|
D:F6T702
|
3.0
|
44.7
|
1.0
|
CB
|
D:ARG515
|
3.1
|
36.0
|
1.0
|
CAV
|
D:F6T702
|
3.6
|
42.7
|
1.0
|
CAX
|
D:F6T702
|
3.6
|
42.1
|
1.0
|
C
|
D:MET514
|
3.6
|
29.7
|
1.0
|
CAW
|
D:F6T702
|
4.0
|
44.5
|
1.0
|
O
|
D:MET514
|
4.1
|
26.3
|
1.0
|
O
|
D:ILE511
|
4.2
|
30.9
|
1.0
|
CG
|
D:ARG515
|
4.3
|
35.4
|
1.0
|
NE
|
D:ARG515
|
4.4
|
34.9
|
1.0
|
C
|
D:ARG515
|
4.4
|
40.4
|
1.0
|
CAD
|
D:F6T702
|
4.5
|
36.8
|
1.0
|
CA
|
D:MET514
|
4.5
|
29.8
|
1.0
|
CB
|
D:MET514
|
4.5
|
29.7
|
1.0
|
O
|
D:ALA512
|
4.5
|
36.1
|
1.0
|
FAY
|
D:F6T702
|
4.6
|
42.9
|
1.0
|
N
|
D:MET514
|
4.8
|
28.2
|
1.0
|
CD
|
D:ARG515
|
4.9
|
36.0
|
1.0
|
O
|
D:GLY525
|
4.9
|
35.2
|
1.0
|
O
|
D:ARG515
|
5.0
|
40.7
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 2 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F702
b:42.9
occ:1.00
|
FAY
|
D:F6T702
|
0.0
|
42.9
|
1.0
|
CAX
|
D:F6T702
|
1.2
|
42.1
|
1.0
|
CAW
|
D:F6T702
|
2.2
|
44.5
|
1.0
|
CAR
|
D:F6T702
|
2.3
|
43.0
|
1.0
|
CAB
|
D:F6T702
|
2.8
|
43.4
|
1.0
|
C
|
D:GLU526
|
3.0
|
30.5
|
1.0
|
O
|
D:GLU526
|
3.2
|
25.7
|
1.0
|
N
|
D:SER527
|
3.3
|
29.2
|
1.0
|
N
|
D:GLU526
|
3.3
|
35.2
|
1.0
|
CA
|
D:GLU526
|
3.3
|
35.2
|
1.0
|
CAV
|
D:F6T702
|
3.5
|
42.7
|
1.0
|
CAS
|
D:F6T702
|
3.5
|
44.6
|
1.0
|
CD1
|
D:TYR580
|
3.6
|
39.9
|
1.0
|
C
|
D:GLY525
|
3.8
|
36.6
|
1.0
|
O
|
D:PHE581
|
3.8
|
30.9
|
1.0
|
CAA
|
D:F6T702
|
3.8
|
44.7
|
1.0
|
CAU
|
D:F6T702
|
4.0
|
44.5
|
1.0
|
CAC
|
D:F6T702
|
4.0
|
40.7
|
1.0
|
CA
|
D:SER527
|
4.0
|
28.0
|
1.0
|
CB
|
D:TYR580
|
4.1
|
34.2
|
1.0
|
N
|
D:PHE581
|
4.1
|
31.3
|
1.0
|
CG
|
D:TYR580
|
4.2
|
38.4
|
1.0
|
CA
|
D:TYR580
|
4.2
|
32.8
|
1.0
|
O
|
D:GLY525
|
4.2
|
35.2
|
1.0
|
OAQ
|
D:F6T702
|
4.3
|
34.4
|
1.0
|
CB
|
D:SER527
|
4.4
|
27.9
|
1.0
|
CE1
|
D:TYR580
|
4.4
|
44.1
|
1.0
|
CA
|
D:GLY525
|
4.5
|
38.1
|
1.0
|
C
|
D:PHE581
|
4.6
|
30.9
|
1.0
|
FAT
|
D:F6T702
|
4.6
|
47.6
|
1.0
|
C
|
D:TYR580
|
4.7
|
31.0
|
1.0
|
CAD
|
D:F6T702
|
4.7
|
36.8
|
1.0
|
CB
|
D:GLU526
|
4.9
|
37.5
|
1.0
|
CA
|
D:PHE581
|
5.0
|
32.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 3 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F702
b:49.2
occ:1.00
|
FAT
|
A:F6T702
|
0.0
|
49.2
|
1.0
|
CAS
|
A:F6T702
|
1.3
|
48.5
|
1.0
|
CAU
|
A:F6T702
|
2.3
|
49.0
|
1.0
|
CAR
|
A:F6T702
|
2.4
|
45.5
|
1.0
|
N
|
A:ARG515
|
2.8
|
38.8
|
1.0
|
CAB
|
A:F6T702
|
2.9
|
46.5
|
1.0
|
CA
|
A:ARG515
|
3.0
|
39.1
|
1.0
|
CAC
|
A:F6T702
|
3.0
|
46.1
|
1.0
|
CAA
|
A:F6T702
|
3.2
|
48.2
|
1.0
|
CB
|
A:ARG515
|
3.2
|
39.7
|
1.0
|
C
|
A:MET514
|
3.4
|
34.9
|
1.0
|
CAV
|
A:F6T702
|
3.6
|
47.8
|
1.0
|
CAX
|
A:F6T702
|
3.7
|
45.1
|
1.0
|
O
|
A:ILE511
|
3.9
|
27.8
|
1.0
|
O
|
A:MET514
|
4.0
|
34.7
|
1.0
|
CAW
|
A:F6T702
|
4.1
|
49.2
|
1.0
|
CB
|
A:MET514
|
4.2
|
34.8
|
1.0
|
CA
|
A:MET514
|
4.2
|
33.0
|
1.0
|
O
|
A:ALA512
|
4.4
|
24.8
|
1.0
|
C
|
A:ARG515
|
4.5
|
36.7
|
1.0
|
CAD
|
A:F6T702
|
4.5
|
44.2
|
1.0
|
N
|
A:MET514
|
4.5
|
29.2
|
1.0
|
CG
|
A:ARG515
|
4.5
|
39.5
|
1.0
|
NE
|
A:ARG515
|
4.7
|
35.2
|
1.0
|
C
|
A:ALA512
|
4.9
|
24.8
|
1.0
|
FAY
|
A:F6T702
|
4.9
|
40.2
|
1.0
|
C
|
A:ILE511
|
5.0
|
28.2
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 4 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F702
b:40.2
occ:1.00
|
FAY
|
A:F6T702
|
0.0
|
40.2
|
1.0
|
CAX
|
A:F6T702
|
1.4
|
45.1
|
1.0
|
CAW
|
A:F6T702
|
2.4
|
49.2
|
1.0
|
CAR
|
A:F6T702
|
2.5
|
45.5
|
1.0
|
CAB
|
A:F6T702
|
2.8
|
46.5
|
1.0
|
C
|
A:GLU526
|
2.9
|
30.0
|
1.0
|
O
|
A:GLU526
|
3.1
|
28.9
|
1.0
|
N
|
A:SER527
|
3.2
|
29.2
|
1.0
|
N
|
A:GLU526
|
3.3
|
36.5
|
1.0
|
CA
|
A:GLU526
|
3.3
|
33.1
|
1.0
|
CD1
|
A:TYR580
|
3.6
|
44.7
|
1.0
|
CAA
|
A:F6T702
|
3.7
|
48.2
|
1.0
|
CAS
|
A:F6T702
|
3.7
|
48.5
|
1.0
|
CAV
|
A:F6T702
|
3.7
|
47.8
|
1.0
|
C
|
A:GLY525
|
3.8
|
39.7
|
1.0
|
O
|
A:PHE581
|
3.8
|
43.0
|
1.0
|
CA
|
A:SER527
|
3.9
|
28.6
|
1.0
|
N
|
A:PHE581
|
4.0
|
39.4
|
1.0
|
CB
|
A:TYR580
|
4.0
|
40.2
|
1.0
|
CAC
|
A:F6T702
|
4.1
|
46.1
|
1.0
|
CA
|
A:TYR580
|
4.1
|
37.8
|
1.0
|
O
|
A:GLY525
|
4.2
|
38.6
|
1.0
|
CG
|
A:TYR580
|
4.2
|
42.0
|
1.0
|
CAU
|
A:F6T702
|
4.2
|
49.0
|
1.0
|
CB
|
A:SER527
|
4.3
|
29.7
|
1.0
|
OAQ
|
A:F6T702
|
4.4
|
45.6
|
1.0
|
CE1
|
A:TYR580
|
4.5
|
47.4
|
1.0
|
CA
|
A:GLY525
|
4.5
|
41.6
|
1.0
|
C
|
A:PHE581
|
4.6
|
41.4
|
1.0
|
C
|
A:TYR580
|
4.6
|
38.8
|
1.0
|
CAD
|
A:F6T702
|
4.7
|
44.2
|
1.0
|
CB
|
A:GLU526
|
4.8
|
32.3
|
1.0
|
FAT
|
A:F6T702
|
4.9
|
49.2
|
1.0
|
CA
|
A:PHE581
|
4.9
|
40.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 5 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F702
b:83.0
occ:1.00
|
FAT
|
B:F6T702
|
0.0
|
83.0
|
1.0
|
CAS
|
B:F6T702
|
1.2
|
83.2
|
1.0
|
CAU
|
B:F6T702
|
2.2
|
82.6
|
1.0
|
CAR
|
B:F6T702
|
2.3
|
80.0
|
1.0
|
CAC
|
B:F6T702
|
2.8
|
73.8
|
1.0
|
CAB
|
B:F6T702
|
2.9
|
78.2
|
1.0
|
CA
|
B:ARG515
|
2.9
|
59.6
|
1.0
|
CB
|
B:ARG515
|
3.0
|
58.9
|
1.0
|
N
|
B:ARG515
|
3.2
|
57.0
|
1.0
|
CAV
|
B:F6T702
|
3.5
|
79.8
|
1.0
|
CAA
|
B:F6T702
|
3.5
|
78.7
|
1.0
|
CAX
|
B:F6T702
|
3.5
|
80.0
|
1.0
|
C
|
B:MET514
|
4.0
|
52.6
|
1.0
|
CAW
|
B:F6T702
|
4.0
|
81.6
|
1.0
|
NE
|
B:ARG515
|
4.0
|
61.1
|
1.0
|
CG
|
B:ARG515
|
4.1
|
60.1
|
1.0
|
O
|
B:GLY525
|
4.3
|
72.6
|
1.0
|
CAD
|
B:F6T702
|
4.4
|
66.6
|
1.0
|
O
|
B:MET514
|
4.4
|
52.9
|
1.0
|
C
|
B:ARG515
|
4.4
|
64.9
|
1.0
|
CD
|
B:ARG515
|
4.6
|
60.0
|
1.0
|
FAY
|
B:F6T702
|
4.7
|
83.3
|
1.0
|
O
|
B:ILE511
|
4.7
|
45.4
|
1.0
|
CZ
|
B:ARG515
|
4.8
|
61.7
|
1.0
|
NH2
|
B:ARG515
|
4.8
|
60.1
|
1.0
|
O
|
B:ALA512
|
4.9
|
46.8
|
1.0
|
O
|
B:ARG515
|
4.9
|
75.8
|
1.0
|
CA
|
B:MET514
|
4.9
|
49.8
|
1.0
|
CB
|
B:MET514
|
4.9
|
48.2
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6gou
Go back to
Fluorine Binding Sites List in 6gou
Fluorine binding site 6 out
of 6 in the Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F702
b:83.3
occ:1.00
|
FAY
|
B:F6T702
|
0.0
|
83.3
|
1.0
|
CAX
|
B:F6T702
|
1.3
|
80.0
|
1.0
|
CAW
|
B:F6T702
|
2.3
|
81.6
|
1.0
|
CAR
|
B:F6T702
|
2.4
|
80.0
|
1.0
|
CAB
|
B:F6T702
|
2.9
|
78.2
|
1.0
|
CD1
|
B:TYR580
|
3.1
|
58.5
|
1.0
|
C
|
B:GLU526
|
3.4
|
48.9
|
1.0
|
O
|
B:GLU526
|
3.5
|
43.6
|
1.0
|
CAA
|
B:F6T702
|
3.5
|
78.7
|
1.0
|
CB
|
B:TYR580
|
3.5
|
53.6
|
1.0
|
CAV
|
B:F6T702
|
3.6
|
79.8
|
1.0
|
N
|
B:SER527
|
3.6
|
49.7
|
1.0
|
CAS
|
B:F6T702
|
3.6
|
83.2
|
1.0
|
CG
|
B:TYR580
|
3.6
|
58.2
|
1.0
|
CA
|
B:TYR580
|
3.8
|
49.9
|
1.0
|
N
|
B:GLU526
|
3.8
|
56.8
|
1.0
|
N
|
B:PHE581
|
3.9
|
47.9
|
1.0
|
CA
|
B:GLU526
|
3.9
|
54.2
|
1.0
|
O
|
B:PHE581
|
4.0
|
60.9
|
1.0
|
CE1
|
B:TYR580
|
4.1
|
64.8
|
1.0
|
CAU
|
B:F6T702
|
4.1
|
82.6
|
1.0
|
CA
|
B:SER527
|
4.2
|
45.9
|
1.0
|
CAC
|
B:F6T702
|
4.3
|
73.8
|
1.0
|
C
|
B:GLY525
|
4.3
|
62.6
|
1.0
|
C
|
B:TYR580
|
4.3
|
49.3
|
1.0
|
CB
|
B:SER527
|
4.5
|
45.2
|
1.0
|
C
|
B:PHE581
|
4.5
|
54.9
|
1.0
|
FAT
|
B:F6T702
|
4.7
|
83.0
|
1.0
|
O
|
B:GLY525
|
4.8
|
72.6
|
1.0
|
CA
|
B:PHE581
|
4.9
|
49.9
|
1.0
|
CD2
|
B:TYR580
|
4.9
|
63.9
|
1.0
|
CA
|
B:GLY525
|
4.9
|
67.0
|
1.0
|
OAQ
|
B:F6T702
|
5.0
|
60.8
|
1.0
|
|
Reference:
G.Stazi,
C.Battistelli,
V.Piano,
R.Mazzone,
B.Marrocco,
S.Marchese,
S.M.Louie,
C.Zwergel,
L.Antonini,
A.Patsilinakos,
R.Ragno,
M.Viviano,
G.Sbardella,
A.Ciogli,
G.Fabrizi,
R.Cirilli,
R.Strippoli,
A.Marchetti,
M.Tripodi,
D.K.Nomura,
A.Mattevi,
A.Mai,
S.Valente.
Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Structure-Activity Relationship and Effects on Ether Lipids and Epithelial-Mesenchymal Transition in Cancer Cells. Eur J Med Chem V. 163 722 2018.
ISSN: ISSN 1768-3254
PubMed: 30576903
DOI: 10.1016/J.EJMECH.2018.11.050
Page generated: Thu Aug 1 20:34:18 2024
|