Fluorine in PDB 6zpl: Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Enzymatic activity of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
All present enzymatic activity of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.:
3.2.1.4;
Protein crystallography data
The structure of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions., PDB code: 6zpl
was solved by
A.Shahsavar,
P.Stohler,
G.Bourenkov,
I.Zimmermann,
M.Siegrist,
W.Guba,
E.Pinard,
S.Sinning,
M.A.Seeger,
T.R.Schneider,
R.J.P.Dawson,
P.Nissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.07 /
3.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.41,
69.71,
149.43,
90,
92.86,
90
|
R / Rfree (%)
|
27.7 /
29.1
|
Other elements in 6zpl:
The structure of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. also contains other interesting chemical elements:
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
(pdb code 6zpl). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions., PDB code: 6zpl:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 1 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:94.2
occ:1.00
|
F01
|
B:QET701
|
0.0
|
94.2
|
1.0
|
C07
|
B:QET701
|
1.4
|
93.0
|
1.0
|
F02
|
B:QET701
|
2.2
|
93.6
|
1.0
|
C06
|
B:QET701
|
2.3
|
91.9
|
1.0
|
C08
|
B:QET701
|
2.4
|
92.8
|
1.0
|
HA3
|
B:GLY378
|
2.4
|
78.5
|
1.0
|
H16
|
B:QET701
|
2.5
|
97.5
|
1.0
|
F04
|
B:QET701
|
2.6
|
93.2
|
1.0
|
HB2
|
B:TRP376
|
2.6
|
74.9
|
1.0
|
H08
|
B:QET701
|
2.7
|
96.8
|
1.0
|
H
|
B:GLY378
|
2.9
|
80.3
|
1.0
|
F05
|
B:QET701
|
3.1
|
93.7
|
1.0
|
CA
|
B:GLY378
|
3.2
|
72.7
|
1.0
|
N
|
B:GLY378
|
3.5
|
73.3
|
1.0
|
CB
|
B:TRP376
|
3.5
|
70.4
|
1.0
|
F03
|
B:QET701
|
3.5
|
91.5
|
1.0
|
H
|
B:LEU379
|
3.5
|
81.7
|
1.0
|
O03
|
B:QET701
|
3.6
|
91.1
|
1.0
|
HB3
|
B:TRP376
|
3.6
|
74.7
|
1.0
|
HG
|
B:LEU379
|
3.7
|
79.4
|
1.0
|
C
|
B:GLY378
|
3.8
|
73.4
|
1.0
|
N
|
B:LEU379
|
3.8
|
73.6
|
1.0
|
O
|
B:GLY373
|
3.8
|
71.0
|
1.0
|
HD21
|
B:LEU379
|
3.9
|
77.1
|
1.0
|
HA3
|
B:GLY373
|
3.9
|
71.3
|
1.0
|
CG
|
B:TRP376
|
4.0
|
69.2
|
1.0
|
HA2
|
B:GLY373
|
4.1
|
70.5
|
1.0
|
HA2
|
B:GLY378
|
4.1
|
80.6
|
1.0
|
HE3
|
B:TRP376
|
4.2
|
68.3
|
1.0
|
CD2
|
B:TRP376
|
4.2
|
67.7
|
1.0
|
H17
|
B:QET701
|
4.3
|
98.4
|
1.0
|
CE3
|
B:TRP376
|
4.4
|
67.1
|
1.0
|
CA
|
B:GLY373
|
4.4
|
68.8
|
1.0
|
H
|
B:GLY377
|
4.6
|
83.4
|
1.0
|
CD2
|
B:LEU379
|
4.6
|
71.6
|
1.0
|
C
|
B:GLY373
|
4.6
|
70.4
|
1.0
|
CG
|
B:LEU379
|
4.6
|
72.8
|
1.0
|
HD22
|
B:LEU379
|
4.6
|
76.5
|
1.0
|
O
|
B:GLY378
|
4.7
|
74.2
|
1.0
|
N
|
B:GLY377
|
4.7
|
74.4
|
1.0
|
C
|
B:GLY377
|
4.7
|
75.2
|
1.0
|
CD1
|
B:TRP376
|
4.7
|
69.2
|
1.0
|
CA
|
B:TRP376
|
4.7
|
72.3
|
1.0
|
HG23
|
B:THR479
|
4.7
|
82.0
|
1.0
|
H02
|
B:QET701
|
4.7
|
93.4
|
1.0
|
H
|
B:TRP376
|
4.8
|
79.9
|
1.0
|
C05
|
B:QET701
|
4.8
|
90.2
|
1.0
|
C
|
B:TRP376
|
4.8
|
73.6
|
1.0
|
HD13
|
B:LEU476
|
4.9
|
70.5
|
1.0
|
CA
|
B:LEU379
|
4.9
|
74.6
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 2 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:93.6
occ:1.00
|
F02
|
B:QET701
|
0.0
|
93.6
|
1.0
|
C07
|
B:QET701
|
1.4
|
93.0
|
1.0
|
F01
|
B:QET701
|
2.2
|
94.2
|
1.0
|
C06
|
B:QET701
|
2.3
|
91.9
|
1.0
|
C08
|
B:QET701
|
2.4
|
92.8
|
1.0
|
H17
|
B:QET701
|
2.5
|
98.4
|
1.0
|
F05
|
B:QET701
|
2.6
|
93.7
|
1.0
|
H16
|
B:QET701
|
2.6
|
97.5
|
1.0
|
O03
|
B:QET701
|
2.6
|
91.1
|
1.0
|
HD21
|
B:LEU379
|
2.9
|
77.1
|
1.0
|
F03
|
B:QET701
|
3.1
|
91.5
|
1.0
|
H08
|
B:QET701
|
3.1
|
96.8
|
1.0
|
HA3
|
B:GLY378
|
3.2
|
78.5
|
1.0
|
C11
|
B:QET701
|
3.4
|
92.3
|
1.0
|
F04
|
B:QET701
|
3.5
|
93.2
|
1.0
|
CD2
|
B:LEU379
|
3.8
|
71.6
|
1.0
|
N01
|
B:QET701
|
3.8
|
91.5
|
1.0
|
HD22
|
B:LEU379
|
3.8
|
76.5
|
1.0
|
H10
|
B:QET701
|
3.9
|
98.9
|
1.0
|
C05
|
B:QET701
|
4.0
|
90.2
|
1.0
|
HA3
|
B:GLY373
|
4.0
|
71.3
|
1.0
|
C
|
B:GLY378
|
4.0
|
73.4
|
1.0
|
C12
|
B:QET701
|
4.0
|
93.9
|
1.0
|
H09
|
B:QET701
|
4.0
|
97.8
|
1.0
|
CA
|
B:GLY378
|
4.1
|
72.7
|
1.0
|
HG
|
B:LEU379
|
4.1
|
79.4
|
1.0
|
N
|
B:LEU379
|
4.1
|
73.6
|
1.0
|
C18
|
B:QET701
|
4.2
|
92.6
|
1.0
|
H
|
B:LEU379
|
4.3
|
81.7
|
1.0
|
SD
|
B:MET382
|
4.3
|
71.2
|
1.0
|
HA
|
B:LEU379
|
4.3
|
83.5
|
1.0
|
O
|
B:GLY378
|
4.4
|
74.2
|
1.0
|
C17
|
B:QET701
|
4.5
|
94.0
|
1.0
|
C10
|
B:QET701
|
4.5
|
90.2
|
1.0
|
CG
|
B:LEU379
|
4.5
|
72.8
|
1.0
|
HD23
|
B:LEU379
|
4.6
|
78.5
|
1.0
|
HB3
|
B:CYS475
|
4.6
|
69.4
|
1.0
|
H
|
B:GLY378
|
4.7
|
80.3
|
1.0
|
HG3
|
B:MET382
|
4.7
|
81.1
|
1.0
|
C09
|
B:QET701
|
4.7
|
89.6
|
1.0
|
HA2
|
B:GLY373
|
4.7
|
70.5
|
1.0
|
C13
|
B:QET701
|
4.7
|
95.2
|
1.0
|
HB2
|
B:TRP376
|
4.7
|
74.9
|
1.0
|
CA
|
B:LEU379
|
4.8
|
74.6
|
1.0
|
H03
|
B:QET701
|
4.8
|
104.4
|
1.0
|
H02
|
B:QET701
|
4.8
|
93.4
|
1.0
|
HA2
|
B:GLY378
|
4.8
|
80.6
|
1.0
|
CA
|
B:GLY373
|
4.8
|
68.8
|
1.0
|
C04
|
B:QET701
|
4.9
|
90.0
|
1.0
|
N
|
B:GLY378
|
4.9
|
73.3
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 3 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:91.5
occ:1.00
|
F03
|
B:QET701
|
0.0
|
91.5
|
1.0
|
C08
|
B:QET701
|
1.4
|
92.8
|
1.0
|
F04
|
B:QET701
|
2.2
|
93.2
|
1.0
|
F05
|
B:QET701
|
2.2
|
93.7
|
1.0
|
C07
|
B:QET701
|
2.4
|
93.0
|
1.0
|
O03
|
B:QET701
|
2.6
|
91.1
|
1.0
|
H08
|
B:QET701
|
2.7
|
96.8
|
1.0
|
C06
|
B:QET701
|
2.7
|
91.9
|
1.0
|
HB2
|
B:CYS475
|
2.9
|
67.7
|
1.0
|
HG23
|
B:THR472
|
3.0
|
60.3
|
1.0
|
F02
|
B:QET701
|
3.1
|
93.6
|
1.0
|
HB3
|
B:CYS475
|
3.5
|
69.4
|
1.0
|
F01
|
B:QET701
|
3.5
|
94.2
|
1.0
|
HB2
|
B:LEU476
|
3.6
|
67.2
|
1.0
|
H16
|
B:QET701
|
3.6
|
97.5
|
1.0
|
O
|
B:THR472
|
3.6
|
65.1
|
1.0
|
HA
|
B:LEU476
|
3.7
|
70.5
|
1.0
|
CB
|
B:CYS475
|
3.7
|
67.6
|
1.0
|
C05
|
B:QET701
|
3.7
|
90.2
|
1.0
|
N
|
B:LEU476
|
3.8
|
67.7
|
1.0
|
H
|
B:LEU476
|
3.8
|
68.0
|
1.0
|
C
|
B:CYS475
|
4.0
|
68.4
|
1.0
|
HA
|
B:THR472
|
4.0
|
60.9
|
1.0
|
CG2
|
B:THR472
|
4.1
|
63.5
|
1.0
|
C10
|
B:QET701
|
4.1
|
90.2
|
1.0
|
CA
|
B:LEU476
|
4.1
|
68.2
|
1.0
|
HD13
|
B:LEU476
|
4.2
|
70.5
|
1.0
|
H17
|
B:QET701
|
4.2
|
98.4
|
1.0
|
O04
|
B:QET701
|
4.3
|
89.7
|
1.0
|
HG22
|
B:THR472
|
4.3
|
59.8
|
1.0
|
O
|
B:CYS475
|
4.3
|
69.7
|
1.0
|
C09
|
B:QET701
|
4.3
|
89.6
|
1.0
|
N01
|
B:QET701
|
4.4
|
91.5
|
1.0
|
CB
|
B:LEU476
|
4.4
|
67.3
|
1.0
|
H10
|
B:QET701
|
4.4
|
98.9
|
1.0
|
CA
|
B:CYS475
|
4.4
|
68.1
|
1.0
|
HA3
|
B:GLY378
|
4.5
|
78.5
|
1.0
|
HZ3
|
B:TRP376
|
4.5
|
64.6
|
1.0
|
HE3
|
B:TRP376
|
4.5
|
68.3
|
1.0
|
C
|
B:THR472
|
4.6
|
64.4
|
1.0
|
HG21
|
B:THR472
|
4.6
|
59.4
|
1.0
|
CZ3
|
B:TRP376
|
4.6
|
65.9
|
1.0
|
CE3
|
B:TRP376
|
4.6
|
67.1
|
1.0
|
C04
|
B:QET701
|
4.7
|
90.0
|
1.0
|
CA
|
B:THR472
|
4.7
|
63.8
|
1.0
|
H02
|
B:QET701
|
4.8
|
93.4
|
1.0
|
C11
|
B:QET701
|
4.8
|
92.3
|
1.0
|
C18
|
B:QET701
|
5.0
|
92.6
|
1.0
|
CB
|
B:THR472
|
5.0
|
63.1
|
1.0
|
HG1
|
B:THR472
|
5.0
|
58.9
|
1.0
|
|
Fluorine binding site 4 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 4 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:93.2
occ:1.00
|
F04
|
B:QET701
|
0.0
|
93.2
|
1.0
|
C08
|
B:QET701
|
1.4
|
92.8
|
1.0
|
F03
|
B:QET701
|
2.2
|
91.5
|
1.0
|
F05
|
B:QET701
|
2.2
|
93.7
|
1.0
|
C07
|
B:QET701
|
2.4
|
93.0
|
1.0
|
HA
|
B:LEU476
|
2.6
|
70.5
|
1.0
|
F01
|
B:QET701
|
2.6
|
94.2
|
1.0
|
HD13
|
B:LEU476
|
2.8
|
70.5
|
1.0
|
H08
|
B:QET701
|
2.9
|
96.8
|
1.0
|
HA3
|
B:GLY378
|
3.2
|
78.5
|
1.0
|
C06
|
B:QET701
|
3.2
|
91.9
|
1.0
|
HE3
|
B:TRP376
|
3.2
|
68.3
|
1.0
|
F02
|
B:QET701
|
3.5
|
93.6
|
1.0
|
CA
|
B:LEU476
|
3.5
|
68.2
|
1.0
|
HB2
|
B:LEU476
|
3.5
|
67.2
|
1.0
|
CD1
|
B:LEU476
|
3.7
|
68.7
|
1.0
|
HD11
|
B:LEU476
|
3.7
|
72.2
|
1.0
|
CE3
|
B:TRP376
|
3.8
|
67.1
|
1.0
|
HB3
|
B:TRP376
|
3.8
|
74.7
|
1.0
|
N
|
B:LEU476
|
3.9
|
67.7
|
1.0
|
H16
|
B:QET701
|
3.9
|
97.5
|
1.0
|
H
|
B:GLY378
|
4.0
|
80.3
|
1.0
|
CB
|
B:LEU476
|
4.0
|
67.3
|
1.0
|
O03
|
B:QET701
|
4.0
|
91.1
|
1.0
|
O
|
B:CYS475
|
4.0
|
69.7
|
1.0
|
HB2
|
B:TRP376
|
4.0
|
74.9
|
1.0
|
C
|
B:CYS475
|
4.1
|
68.4
|
1.0
|
HG23
|
B:THR479
|
4.1
|
82.0
|
1.0
|
CA
|
B:GLY378
|
4.2
|
72.7
|
1.0
|
HG1
|
B:THR479
|
4.3
|
78.4
|
1.0
|
HB
|
B:THR479
|
4.3
|
79.8
|
1.0
|
H
|
B:LEU476
|
4.4
|
68.0
|
1.0
|
HZ3
|
B:TRP376
|
4.4
|
64.6
|
1.0
|
CZ3
|
B:TRP376
|
4.4
|
65.9
|
1.0
|
CB
|
B:TRP376
|
4.4
|
70.4
|
1.0
|
CG
|
B:LEU476
|
4.4
|
68.0
|
1.0
|
HB2
|
B:CYS475
|
4.5
|
67.7
|
1.0
|
CD2
|
B:TRP376
|
4.5
|
67.7
|
1.0
|
OG1
|
B:THR479
|
4.5
|
72.5
|
1.0
|
HD12
|
B:LEU476
|
4.5
|
71.6
|
1.0
|
HA2
|
B:GLY378
|
4.6
|
80.6
|
1.0
|
N
|
B:GLY378
|
4.6
|
73.3
|
1.0
|
HB3
|
B:CYS475
|
4.6
|
69.4
|
1.0
|
C
|
B:LEU476
|
4.7
|
69.6
|
1.0
|
HG23
|
B:THR472
|
4.8
|
60.3
|
1.0
|
HD22
|
B:LEU476
|
4.8
|
66.9
|
1.0
|
O
|
B:THR472
|
4.8
|
65.1
|
1.0
|
CG
|
B:TRP376
|
4.8
|
69.2
|
1.0
|
CB
|
B:THR479
|
4.8
|
73.2
|
1.0
|
O
|
B:LEU476
|
4.8
|
70.8
|
1.0
|
CB
|
B:CYS475
|
4.9
|
67.6
|
1.0
|
HB3
|
B:LEU476
|
5.0
|
67.8
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 5 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:93.7
occ:1.00
|
F05
|
B:QET701
|
0.0
|
93.7
|
1.0
|
C08
|
B:QET701
|
1.4
|
92.8
|
1.0
|
F03
|
B:QET701
|
2.2
|
91.5
|
1.0
|
F04
|
B:QET701
|
2.2
|
93.2
|
1.0
|
C07
|
B:QET701
|
2.4
|
93.0
|
1.0
|
F02
|
B:QET701
|
2.6
|
93.6
|
1.0
|
HA3
|
B:GLY378
|
2.7
|
78.5
|
1.0
|
HB3
|
B:CYS475
|
2.8
|
69.4
|
1.0
|
F01
|
B:QET701
|
3.1
|
94.2
|
1.0
|
O
|
B:CYS475
|
3.3
|
69.7
|
1.0
|
HG1
|
B:THR479
|
3.3
|
78.4
|
1.0
|
HB2
|
B:CYS475
|
3.4
|
67.7
|
1.0
|
CB
|
B:CYS475
|
3.5
|
67.6
|
1.0
|
C
|
B:CYS475
|
3.5
|
68.4
|
1.0
|
HA
|
B:LEU476
|
3.6
|
70.5
|
1.0
|
OG1
|
B:THR479
|
3.6
|
72.5
|
1.0
|
C06
|
B:QET701
|
3.7
|
91.9
|
1.0
|
CA
|
B:GLY378
|
3.7
|
72.7
|
1.0
|
HA2
|
B:GLY378
|
3.9
|
80.6
|
1.0
|
H08
|
B:QET701
|
4.0
|
96.8
|
1.0
|
O03
|
B:QET701
|
4.0
|
91.1
|
1.0
|
N
|
B:LEU476
|
4.0
|
67.7
|
1.0
|
HG3
|
B:MET382
|
4.1
|
81.1
|
1.0
|
CA
|
B:CYS475
|
4.1
|
68.1
|
1.0
|
SD
|
B:MET382
|
4.1
|
71.2
|
1.0
|
C
|
B:GLY378
|
4.3
|
73.4
|
1.0
|
CA
|
B:LEU476
|
4.3
|
68.2
|
1.0
|
H10
|
B:QET701
|
4.4
|
98.9
|
1.0
|
H16
|
B:QET701
|
4.4
|
97.5
|
1.0
|
HG23
|
B:THR479
|
4.4
|
82.0
|
1.0
|
HB
|
B:THR479
|
4.4
|
79.8
|
1.0
|
O
|
B:GLY378
|
4.5
|
74.2
|
1.0
|
H
|
B:LEU476
|
4.5
|
68.0
|
1.0
|
HA
|
B:CYS475
|
4.6
|
71.0
|
1.0
|
H17
|
B:QET701
|
4.6
|
98.4
|
1.0
|
CB
|
B:THR479
|
4.6
|
73.2
|
1.0
|
H
|
B:GLY378
|
4.6
|
80.3
|
1.0
|
CG
|
B:MET382
|
4.7
|
73.3
|
1.0
|
N
|
B:GLY378
|
4.8
|
73.3
|
1.0
|
HB2
|
B:LEU476
|
4.8
|
67.2
|
1.0
|
HD13
|
B:LEU476
|
4.9
|
70.5
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 6 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F701
b:98.4
occ:1.00
|
F06
|
B:QET701
|
0.0
|
98.4
|
1.0
|
C14
|
B:QET701
|
1.4
|
96.8
|
1.0
|
C13
|
B:QET701
|
2.4
|
95.2
|
1.0
|
C15
|
B:QET701
|
2.4
|
97.1
|
1.0
|
HD13
|
B:ILE399
|
2.5
|
81.9
|
1.0
|
H03
|
B:QET701
|
2.6
|
104.4
|
1.0
|
HD12
|
B:ILE399
|
2.8
|
84.1
|
1.0
|
O05
|
B:QET701
|
2.8
|
99.0
|
1.0
|
H12
|
B:QET701
|
2.8
|
120.1
|
1.0
|
HD21
|
B:LEU158
|
2.9
|
91.0
|
1.0
|
CD1
|
B:ILE399
|
3.0
|
74.3
|
1.0
|
HZ
|
B:PHE154
|
3.0
|
81.4
|
1.0
|
H20
|
B:QET701
|
3.2
|
120.5
|
1.0
|
C21
|
B:QET701
|
3.3
|
102.5
|
1.0
|
HD11
|
B:ILE399
|
3.3
|
84.6
|
1.0
|
C22
|
B:QET701
|
3.4
|
100.6
|
1.0
|
H06
|
B:QET701
|
3.4
|
115.8
|
1.0
|
HE1
|
B:PHE154
|
3.5
|
80.3
|
1.0
|
HD23
|
B:LEU379
|
3.5
|
78.5
|
1.0
|
C12
|
B:QET701
|
3.6
|
93.9
|
1.0
|
C16
|
B:QET701
|
3.7
|
95.7
|
1.0
|
HG21
|
B:ILE399
|
3.7
|
76.7
|
1.0
|
HD13
|
B:LEU158
|
3.7
|
95.0
|
1.0
|
CZ
|
B:PHE154
|
3.8
|
73.6
|
1.0
|
CD2
|
B:LEU158
|
3.9
|
78.6
|
1.0
|
CE1
|
B:PHE154
|
4.0
|
73.2
|
1.0
|
C17
|
B:QET701
|
4.1
|
94.0
|
1.0
|
HD23
|
B:LEU158
|
4.2
|
93.7
|
1.0
|
CG1
|
B:ILE399
|
4.4
|
74.0
|
1.0
|
H04
|
B:QET701
|
4.4
|
105.8
|
1.0
|
CD2
|
B:LEU379
|
4.4
|
71.6
|
1.0
|
HD2
|
B:TYR116
|
4.5
|
77.8
|
1.0
|
HD22
|
B:LEU158
|
4.5
|
92.3
|
1.0
|
CD1
|
B:LEU158
|
4.5
|
80.5
|
1.0
|
HD22
|
B:LEU379
|
4.5
|
76.5
|
1.0
|
HD12
|
B:LEU158
|
4.6
|
97.7
|
1.0
|
HD21
|
B:LEU379
|
4.7
|
77.1
|
1.0
|
CG2
|
B:ILE399
|
4.7
|
71.3
|
1.0
|
C20
|
B:QET701
|
4.7
|
105.0
|
1.0
|
HG12
|
B:ILE399
|
4.8
|
81.8
|
1.0
|
HB
|
B:ILE399
|
4.8
|
82.8
|
1.0
|
CG
|
B:LEU158
|
4.8
|
80.0
|
1.0
|
C23
|
B:QET701
|
4.8
|
101.4
|
1.0
|
HB3
|
B:TYR116
|
4.9
|
70.0
|
1.0
|
CB
|
B:ILE399
|
4.9
|
73.5
|
1.0
|
CD2
|
B:TYR116
|
4.9
|
71.4
|
1.0
|
CE2
|
B:PHE154
|
4.9
|
74.8
|
1.0
|
H19
|
B:QET701
|
5.0
|
127.1
|
1.0
|
HG
|
B:LEU158
|
5.0
|
95.1
|
1.0
|
H21
|
B:QET701
|
5.0
|
116.9
|
1.0
|
C11
|
B:QET701
|
5.0
|
92.3
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 7 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:100.5
occ:1.00
|
F01
|
A:QET701
|
0.0
|
100.5
|
1.0
|
C07
|
A:QET701
|
1.4
|
100.4
|
1.0
|
F02
|
A:QET701
|
2.2
|
99.7
|
1.0
|
C08
|
A:QET701
|
2.3
|
101.5
|
1.0
|
C06
|
A:QET701
|
2.4
|
100.3
|
1.0
|
H16
|
A:QET701
|
2.4
|
100.9
|
1.0
|
F03
|
A:QET701
|
2.7
|
101.8
|
1.0
|
H10
|
A:QET701
|
2.7
|
99.9
|
1.0
|
F04
|
A:QET701
|
2.8
|
102.3
|
1.0
|
N01
|
A:QET701
|
3.0
|
99.6
|
1.0
|
H08
|
A:QET701
|
3.1
|
101.0
|
1.0
|
O03
|
A:QET701
|
3.1
|
99.3
|
1.0
|
C18
|
A:QET701
|
3.1
|
100.0
|
1.0
|
H17
|
A:QET701
|
3.2
|
101.3
|
1.0
|
C17
|
A:QET701
|
3.4
|
101.3
|
1.0
|
C11
|
A:QET701
|
3.4
|
100.5
|
1.0
|
C10
|
A:QET701
|
3.4
|
98.7
|
1.0
|
F05
|
A:QET701
|
3.5
|
101.5
|
1.0
|
C12
|
A:QET701
|
3.5
|
101.5
|
1.0
|
HB2
|
A:CYS475
|
3.7
|
52.2
|
1.0
|
HB3
|
A:CYS475
|
3.8
|
53.5
|
1.0
|
O04
|
A:QET701
|
3.8
|
98.2
|
1.0
|
H18
|
A:QET701
|
4.0
|
99.9
|
1.0
|
C05
|
A:QET701
|
4.1
|
99.1
|
1.0
|
HG23
|
A:THR472
|
4.1
|
47.5
|
1.0
|
C16
|
A:QET701
|
4.2
|
102.3
|
1.0
|
C09
|
A:QET701
|
4.2
|
98.7
|
1.0
|
CB
|
A:CYS475
|
4.3
|
60.4
|
1.0
|
HD21
|
A:LEU379
|
4.3
|
61.9
|
1.0
|
SD
|
A:MET382
|
4.3
|
63.4
|
1.0
|
H09
|
A:QET701
|
4.4
|
101.2
|
1.0
|
C13
|
A:QET701
|
4.4
|
102.8
|
1.0
|
H04
|
A:QET701
|
4.5
|
105.2
|
1.0
|
HZ3
|
A:TRP376
|
4.6
|
51.8
|
1.0
|
HA3
|
A:GLY378
|
4.8
|
62.2
|
1.0
|
HA
|
A:THR472
|
4.8
|
46.9
|
1.0
|
HE3
|
A:TRP376
|
4.9
|
55.0
|
1.0
|
H03
|
A:QET701
|
4.9
|
106.6
|
1.0
|
HA3
|
A:GLY373
|
4.9
|
59.0
|
1.0
|
HD22
|
A:LEU379
|
4.9
|
61.8
|
1.0
|
HG1
|
A:THR472
|
4.9
|
45.9
|
1.0
|
C15
|
A:QET701
|
5.0
|
103.6
|
1.0
|
|
Fluorine binding site 8 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 8 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:99.7
occ:1.00
|
F02
|
A:QET701
|
0.0
|
99.7
|
1.0
|
C07
|
A:QET701
|
1.4
|
100.4
|
1.0
|
F01
|
A:QET701
|
2.2
|
100.5
|
1.0
|
C08
|
A:QET701
|
2.3
|
101.5
|
1.0
|
C06
|
A:QET701
|
2.4
|
100.3
|
1.0
|
HG23
|
A:THR472
|
2.5
|
47.5
|
1.0
|
O03
|
A:QET701
|
2.5
|
99.3
|
1.0
|
F05
|
A:QET701
|
2.7
|
101.5
|
1.0
|
F03
|
A:QET701
|
2.7
|
101.8
|
1.0
|
HZ3
|
A:TRP376
|
2.7
|
51.8
|
1.0
|
H08
|
A:QET701
|
2.9
|
101.0
|
1.0
|
HB2
|
A:CYS475
|
3.0
|
52.2
|
1.0
|
H16
|
A:QET701
|
3.1
|
100.9
|
1.0
|
CZ3
|
A:TRP376
|
3.4
|
60.2
|
1.0
|
HE3
|
A:TRP376
|
3.5
|
55.0
|
1.0
|
F04
|
A:QET701
|
3.5
|
102.3
|
1.0
|
CG2
|
A:THR472
|
3.6
|
57.8
|
1.0
|
O
|
A:THR472
|
3.6
|
58.6
|
1.0
|
HA
|
A:THR472
|
3.7
|
46.9
|
1.0
|
CE3
|
A:TRP376
|
3.8
|
61.2
|
1.0
|
C05
|
A:QET701
|
3.8
|
99.1
|
1.0
|
HB2
|
A:LEU476
|
3.8
|
52.7
|
1.0
|
HB3
|
A:CYS475
|
3.8
|
53.5
|
1.0
|
HG22
|
A:THR472
|
3.9
|
47.2
|
1.0
|
CB
|
A:CYS475
|
3.9
|
60.4
|
1.0
|
O04
|
A:QET701
|
3.9
|
98.2
|
1.0
|
C10
|
A:QET701
|
4.0
|
98.7
|
1.0
|
HG21
|
A:THR472
|
4.0
|
47.0
|
1.0
|
H
|
A:LEU476
|
4.1
|
52.8
|
1.0
|
H10
|
A:QET701
|
4.2
|
99.9
|
1.0
|
N
|
A:LEU476
|
4.2
|
60.7
|
1.0
|
HA
|
A:LEU476
|
4.2
|
55.2
|
1.0
|
N01
|
A:QET701
|
4.4
|
99.6
|
1.0
|
CA
|
A:THR472
|
4.4
|
57.5
|
1.0
|
HG1
|
A:THR472
|
4.4
|
45.9
|
1.0
|
C09
|
A:QET701
|
4.4
|
98.7
|
1.0
|
C
|
A:THR472
|
4.4
|
58.0
|
1.0
|
C
|
A:CYS475
|
4.5
|
61.2
|
1.0
|
CH2
|
A:TRP376
|
4.5
|
60.0
|
1.0
|
CB
|
A:THR472
|
4.5
|
57.2
|
1.0
|
HD13
|
A:LEU476
|
4.6
|
56.2
|
1.0
|
CA
|
A:LEU476
|
4.6
|
61.3
|
1.0
|
HH2
|
A:TRP376
|
4.6
|
51.3
|
1.0
|
CB
|
A:LEU476
|
4.7
|
60.6
|
1.0
|
H17
|
A:QET701
|
4.7
|
101.3
|
1.0
|
C18
|
A:QET701
|
4.7
|
100.0
|
1.0
|
CA
|
A:CYS475
|
4.8
|
60.9
|
1.0
|
O
|
A:CYS475
|
4.9
|
62.2
|
1.0
|
C04
|
A:QET701
|
4.9
|
99.4
|
1.0
|
OG1
|
A:THR472
|
5.0
|
57.0
|
1.0
|
H02
|
A:QET701
|
5.0
|
99.0
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 9 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:101.8
occ:1.00
|
F03
|
A:QET701
|
0.0
|
101.8
|
1.0
|
C08
|
A:QET701
|
1.4
|
101.5
|
1.0
|
F05
|
A:QET701
|
2.2
|
101.5
|
1.0
|
F04
|
A:QET701
|
2.2
|
102.3
|
1.0
|
C07
|
A:QET701
|
2.3
|
100.4
|
1.0
|
HA3
|
A:GLY378
|
2.5
|
62.2
|
1.0
|
F01
|
A:QET701
|
2.7
|
100.5
|
1.0
|
F02
|
A:QET701
|
2.7
|
99.7
|
1.0
|
HB3
|
A:CYS475
|
3.3
|
53.5
|
1.0
|
CA
|
A:GLY378
|
3.5
|
65.2
|
1.0
|
C06
|
A:QET701
|
3.7
|
100.3
|
1.0
|
HG1
|
A:THR479
|
3.8
|
61.1
|
1.0
|
HE3
|
A:TRP376
|
3.8
|
55.0
|
1.0
|
H08
|
A:QET701
|
3.8
|
101.0
|
1.0
|
HB2
|
A:CYS475
|
3.9
|
52.2
|
1.0
|
O
|
A:CYS475
|
3.9
|
62.2
|
1.0
|
HA2
|
A:GLY378
|
3.9
|
63.8
|
1.0
|
HA
|
A:LEU476
|
3.9
|
55.2
|
1.0
|
OG1
|
A:THR479
|
4.0
|
64.5
|
1.0
|
C
|
A:GLY378
|
4.0
|
65.6
|
1.0
|
CB
|
A:CYS475
|
4.1
|
60.4
|
1.0
|
H16
|
A:QET701
|
4.1
|
100.9
|
1.0
|
C
|
A:CYS475
|
4.1
|
61.2
|
1.0
|
HG3
|
A:MET382
|
4.2
|
63.0
|
1.0
|
H
|
A:GLY378
|
4.3
|
64.3
|
1.0
|
SD
|
A:MET382
|
4.3
|
63.4
|
1.0
|
O
|
A:GLY378
|
4.3
|
65.8
|
1.0
|
HG21
|
A:THR479
|
4.4
|
64.5
|
1.0
|
N
|
A:GLY378
|
4.5
|
65.9
|
1.0
|
N
|
A:LEU476
|
4.5
|
60.7
|
1.0
|
HD21
|
A:LEU379
|
4.6
|
61.9
|
1.0
|
CE3
|
A:TRP376
|
4.6
|
61.2
|
1.0
|
HZ3
|
A:TRP376
|
4.7
|
51.8
|
1.0
|
O03
|
A:QET701
|
4.7
|
99.3
|
1.0
|
N
|
A:LEU379
|
4.7
|
66.0
|
1.0
|
CA
|
A:LEU476
|
4.7
|
61.3
|
1.0
|
CA
|
A:CYS475
|
4.7
|
60.9
|
1.0
|
HB
|
A:THR479
|
4.8
|
62.5
|
1.0
|
CG
|
A:MET382
|
4.8
|
65.0
|
1.0
|
CB
|
A:THR479
|
4.9
|
65.1
|
1.0
|
HB2
|
A:TRP376
|
4.9
|
61.5
|
1.0
|
HD13
|
A:LEU476
|
4.9
|
56.2
|
1.0
|
H
|
A:LEU379
|
4.9
|
65.3
|
1.0
|
H
|
A:LEU476
|
5.0
|
52.8
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 6zpl
Go back to
Fluorine Binding Sites List in 6zpl
Fluorine binding site 10 out
of 12 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:102.3
occ:1.00
|
F04
|
A:QET701
|
0.0
|
102.3
|
1.0
|
C08
|
A:QET701
|
1.4
|
101.5
|
1.0
|
F05
|
A:QET701
|
2.2
|
101.5
|
1.0
|
F03
|
A:QET701
|
2.2
|
101.8
|
1.0
|
C07
|
A:QET701
|
2.3
|
100.4
|
1.0
|
H08
|
A:QET701
|
2.7
|
101.0
|
1.0
|
F01
|
A:QET701
|
2.8
|
100.5
|
1.0
|
C06
|
A:QET701
|
2.8
|
100.3
|
1.0
|
HA3
|
A:GLY378
|
2.8
|
62.2
|
1.0
|
H16
|
A:QET701
|
2.9
|
100.9
|
1.0
|
HD21
|
A:LEU379
|
3.0
|
61.9
|
1.0
|
HA3
|
A:GLY373
|
3.5
|
59.0
|
1.0
|
F02
|
A:QET701
|
3.5
|
99.7
|
1.0
|
HG
|
A:LEU379
|
3.5
|
64.5
|
1.0
|
CA
|
A:GLY378
|
3.7
|
65.2
|
1.0
|
H
|
A:LEU379
|
3.7
|
65.3
|
1.0
|
HE3
|
A:TRP376
|
3.7
|
55.0
|
1.0
|
HB2
|
A:TRP376
|
3.7
|
61.5
|
1.0
|
N
|
A:LEU379
|
3.7
|
66.0
|
1.0
|
C
|
A:GLY378
|
3.7
|
65.6
|
1.0
|
CD2
|
A:LEU379
|
3.8
|
64.8
|
1.0
|
HD22
|
A:LEU379
|
3.8
|
61.8
|
1.0
|
H
|
A:GLY378
|
3.9
|
64.3
|
1.0
|
HA2
|
A:GLY373
|
4.1
|
58.6
|
1.0
|
O
|
A:GLY373
|
4.1
|
65.0
|
1.0
|
CG
|
A:LEU379
|
4.2
|
65.9
|
1.0
|
O03
|
A:QET701
|
4.2
|
99.3
|
1.0
|
CE3
|
A:TRP376
|
4.2
|
61.2
|
1.0
|
CA
|
A:GLY373
|
4.2
|
63.3
|
1.0
|
N
|
A:GLY378
|
4.2
|
65.9
|
1.0
|
HA
|
A:LEU379
|
4.4
|
66.3
|
1.0
|
O
|
A:GLY378
|
4.4
|
65.8
|
1.0
|
H17
|
A:QET701
|
4.5
|
101.3
|
1.0
|
HA2
|
A:GLY378
|
4.5
|
63.8
|
1.0
|
CA
|
A:LEU379
|
4.6
|
66.8
|
1.0
|
CD2
|
A:TRP376
|
4.6
|
62.2
|
1.0
|
CB
|
A:TRP376
|
4.6
|
64.4
|
1.0
|
C
|
A:GLY373
|
4.7
|
64.7
|
1.0
|
HD23
|
A:LEU379
|
4.7
|
63.1
|
1.0
|
HB3
|
A:TRP376
|
4.8
|
61.3
|
1.0
|
CZ3
|
A:TRP376
|
4.8
|
60.2
|
1.0
|
HZ3
|
A:TRP376
|
4.9
|
51.8
|
1.0
|
CG
|
A:TRP376
|
4.9
|
63.6
|
1.0
|
CB
|
A:LEU379
|
4.9
|
67.2
|
1.0
|
C12
|
A:QET701
|
5.0
|
101.5
|
1.0
|
|
Reference:
A.Shahsavar,
P.Stohler,
G.Bourenkov,
I.Zimmermann,
M.Siegrist,
W.Guba,
E.Pinard,
S.Sinning,
M.A.Seeger,
T.R.Schneider,
R.J.P.Dawson,
P.Nissen.
Structural Insights Into the Inhibition of Glycine Reuptake. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33658720
DOI: 10.1038/S41586-021-03274-Z
Page generated: Fri Aug 2 05:20:23 2024
|