Fluorine in PDB 6xf3: Crystal Structure of Sting in Complex with E7766
Protein crystallography data
The structure of Crystal Structure of Sting in Complex with E7766, PDB code: 6xf3
was solved by
Y.Chen,
J.Y.Wang,
D.-S.Kim,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.46 /
2.38
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
33.82,
78.11,
132.212,
90,
90,
90
|
|
R / Rfree (%)
|
20.8 /
26.1
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Sting in Complex with E7766
(pdb code 6xf3). 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 Sting in Complex with E7766, PDB code: 6xf3:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6xf3
Go back to
Fluorine Binding Sites List in 6xf3
Fluorine binding site 1 out
of 4 in the Crystal Structure of Sting in Complex with E7766
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Sting in Complex with E7766 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.3
occ:0.50
|
F1
|
A:V5V401
|
0.0
|
13.3
|
0.5
|
|
F1
|
A:V5V401
|
0.1
|
13.8
|
0.5
|
|
C
|
A:V5V401
|
1.3
|
13.6
|
0.5
|
|
C
|
A:V5V401
|
1.4
|
13.2
|
0.5
|
|
C3
|
A:V5V401
|
2.3
|
13.6
|
0.5
|
|
C1
|
A:V5V401
|
2.3
|
13.6
|
0.5
|
|
C1
|
A:V5V401
|
2.3
|
13.2
|
0.5
|
|
C3
|
A:V5V401
|
2.4
|
13.1
|
0.5
|
|
C2
|
A:V5V401
|
2.6
|
13.6
|
0.5
|
|
O1
|
A:V5V401
|
2.6
|
13.7
|
0.5
|
|
O1
|
A:V5V401
|
2.7
|
13.1
|
0.5
|
|
C2
|
A:V5V401
|
2.8
|
13.1
|
0.5
|
|
O
|
A:V5V401
|
2.9
|
13.6
|
0.5
|
|
O
|
A:V5V401
|
3.0
|
13.2
|
0.5
|
|
CD
|
A:PRO264
|
3.2
|
16.0
|
1.0
|
|
CG
|
A:PRO264
|
3.3
|
16.3
|
1.0
|
|
CD1
|
A:TYR163
|
3.3
|
12.7
|
1.0
|
|
O
|
A:HOH531
|
3.4
|
11.5
|
1.0
|
|
N
|
A:V5V401
|
3.6
|
13.7
|
0.5
|
|
N
|
A:V5V401
|
3.6
|
13.3
|
0.5
|
|
CE1
|
A:TYR163
|
3.7
|
12.4
|
1.0
|
|
O3
|
A:V5V401
|
3.7
|
13.5
|
0.5
|
|
CB
|
A:THR263
|
3.7
|
15.0
|
1.0
|
|
P
|
A:V5V401
|
3.7
|
13.6
|
0.5
|
|
P
|
A:V5V401
|
3.8
|
13.0
|
0.5
|
|
N
|
A:PRO264
|
4.0
|
16.1
|
1.0
|
|
S1
|
A:V5V401
|
4.0
|
12.9
|
0.5
|
|
OG1
|
A:THR263
|
4.1
|
15.0
|
1.0
|
|
C4
|
A:V5V401
|
4.1
|
13.6
|
0.5
|
|
N2
|
A:V5V401
|
4.2
|
13.3
|
0.5
|
|
N2
|
A:V5V401
|
4.2
|
13.7
|
0.5
|
|
C5
|
A:V5V401
|
4.3
|
13.3
|
0.5
|
|
C5
|
A:V5V401
|
4.3
|
13.7
|
0.5
|
|
C4
|
A:V5V401
|
4.3
|
13.1
|
0.5
|
|
CA
|
A:THR263
|
4.4
|
15.3
|
1.0
|
|
N
|
A:THR263
|
4.4
|
15.0
|
1.0
|
|
C
|
A:THR263
|
4.5
|
15.5
|
1.0
|
|
O
|
A:HOH548
|
4.5
|
26.9
|
1.0
|
|
CG
|
A:TYR163
|
4.5
|
12.8
|
1.0
|
|
C7
|
A:V5V401
|
4.6
|
13.7
|
0.5
|
|
O3
|
A:V5V401
|
4.6
|
13.0
|
0.5
|
|
C7
|
A:V5V401
|
4.7
|
13.3
|
0.5
|
|
CB
|
A:PRO264
|
4.7
|
16.4
|
1.0
|
|
CG2
|
A:THR263
|
4.7
|
15.2
|
1.0
|
|
O
|
A:HOH501
|
4.7
|
23.7
|
1.0
|
|
O2
|
A:V5V401
|
4.8
|
13.6
|
0.5
|
|
CA
|
A:PRO264
|
4.8
|
16.5
|
1.0
|
|
S1
|
A:V5V401
|
4.9
|
13.8
|
0.5
|
|
O6
|
A:V5V401
|
4.9
|
13.6
|
0.5
|
|
O6
|
A:V5V401
|
4.9
|
13.1
|
0.5
|
|
CB
|
A:TYR163
|
5.0
|
13.1
|
1.0
|
|
O2
|
A:V5V401
|
5.0
|
13.1
|
0.5
|
|
Fluorine binding site 2 out
of 4 in 6xf3
Go back to
Fluorine Binding Sites List in 6xf3
Fluorine binding site 2 out
of 4 in the Crystal Structure of Sting in Complex with E7766
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Sting in Complex with E7766 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.8
occ:0.50
|
F1
|
A:V5V401
|
0.0
|
13.8
|
0.5
|
|
F1
|
A:V5V401
|
0.1
|
13.3
|
0.5
|
|
C
|
A:V5V401
|
1.4
|
13.6
|
0.5
|
|
C
|
A:V5V401
|
1.4
|
13.2
|
0.5
|
|
C1
|
A:V5V401
|
2.3
|
13.6
|
0.5
|
|
C3
|
A:V5V401
|
2.4
|
13.6
|
0.5
|
|
C1
|
A:V5V401
|
2.4
|
13.2
|
0.5
|
|
C3
|
A:V5V401
|
2.4
|
13.1
|
0.5
|
|
O1
|
A:V5V401
|
2.7
|
13.7
|
0.5
|
|
C2
|
A:V5V401
|
2.8
|
13.6
|
0.5
|
|
O1
|
A:V5V401
|
2.8
|
13.1
|
0.5
|
|
C2
|
A:V5V401
|
2.9
|
13.1
|
0.5
|
|
O
|
A:V5V401
|
2.9
|
13.6
|
0.5
|
|
O
|
A:V5V401
|
3.0
|
13.2
|
0.5
|
|
CD
|
A:PRO264
|
3.2
|
16.0
|
1.0
|
|
O
|
A:HOH531
|
3.2
|
11.5
|
1.0
|
|
CD1
|
A:TYR163
|
3.3
|
12.7
|
1.0
|
|
CG
|
A:PRO264
|
3.3
|
16.3
|
1.0
|
|
N
|
A:V5V401
|
3.6
|
13.7
|
0.5
|
|
N
|
A:V5V401
|
3.6
|
13.3
|
0.5
|
|
CB
|
A:THR263
|
3.6
|
15.0
|
1.0
|
|
CE1
|
A:TYR163
|
3.6
|
12.4
|
1.0
|
|
O3
|
A:V5V401
|
3.7
|
13.5
|
0.5
|
|
P
|
A:V5V401
|
3.8
|
13.6
|
0.5
|
|
P
|
A:V5V401
|
3.9
|
13.0
|
0.5
|
|
N
|
A:PRO264
|
4.0
|
16.1
|
1.0
|
|
S1
|
A:V5V401
|
4.0
|
12.9
|
0.5
|
|
OG1
|
A:THR263
|
4.0
|
15.0
|
1.0
|
|
N2
|
A:V5V401
|
4.1
|
13.3
|
0.5
|
|
N2
|
A:V5V401
|
4.1
|
13.7
|
0.5
|
|
C4
|
A:V5V401
|
4.3
|
13.6
|
0.5
|
|
C5
|
A:V5V401
|
4.3
|
13.3
|
0.5
|
|
C5
|
A:V5V401
|
4.3
|
13.7
|
0.5
|
|
CA
|
A:THR263
|
4.3
|
15.3
|
1.0
|
|
N
|
A:THR263
|
4.3
|
15.0
|
1.0
|
|
C4
|
A:V5V401
|
4.4
|
13.1
|
0.5
|
|
C
|
A:THR263
|
4.4
|
15.5
|
1.0
|
|
CG
|
A:TYR163
|
4.6
|
12.8
|
1.0
|
|
CG2
|
A:THR263
|
4.6
|
15.2
|
1.0
|
|
O
|
A:HOH548
|
4.6
|
26.9
|
1.0
|
|
C7
|
A:V5V401
|
4.6
|
13.7
|
0.5
|
|
C7
|
A:V5V401
|
4.7
|
13.3
|
0.5
|
|
O3
|
A:V5V401
|
4.7
|
13.0
|
0.5
|
|
CB
|
A:PRO264
|
4.7
|
16.4
|
1.0
|
|
O
|
A:HOH501
|
4.8
|
23.7
|
1.0
|
|
CA
|
A:PRO264
|
4.8
|
16.5
|
1.0
|
|
O2
|
A:V5V401
|
4.9
|
13.6
|
0.5
|
|
S1
|
A:V5V401
|
4.9
|
13.8
|
0.5
|
|
NH1
|
B:ARG238
|
4.9
|
20.1
|
0.5
|
|
CZ
|
A:TYR163
|
5.0
|
12.3
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6xf3
Go back to
Fluorine Binding Sites List in 6xf3
Fluorine binding site 3 out
of 4 in the Crystal Structure of Sting in Complex with E7766
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Sting in Complex with E7766 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.3
occ:0.50
|
F
|
A:V5V401
|
0.0
|
13.3
|
0.5
|
|
F
|
A:V5V401
|
0.0
|
13.7
|
0.5
|
|
C10
|
A:V5V401
|
1.4
|
13.2
|
0.5
|
|
C10
|
A:V5V401
|
1.4
|
13.6
|
0.5
|
|
C13
|
A:V5V401
|
2.3
|
13.2
|
0.5
|
|
C13
|
A:V5V401
|
2.4
|
13.6
|
0.5
|
|
C11
|
A:V5V401
|
2.4
|
13.2
|
0.5
|
|
C11
|
A:V5V401
|
2.4
|
13.6
|
0.5
|
|
O5
|
A:V5V401
|
2.7
|
13.6
|
0.5
|
|
C12
|
A:V5V401
|
2.8
|
13.2
|
0.5
|
|
O5
|
A:V5V401
|
2.8
|
13.2
|
0.5
|
|
C12
|
A:V5V401
|
2.9
|
13.6
|
0.5
|
|
O4
|
A:V5V401
|
3.0
|
13.1
|
0.5
|
|
O4
|
A:V5V401
|
3.1
|
13.5
|
0.5
|
|
CD
|
B:PRO264
|
3.2
|
16.2
|
1.0
|
|
O
|
B:HOH417
|
3.3
|
14.2
|
1.0
|
|
CD1
|
B:TYR163
|
3.3
|
13.9
|
1.0
|
|
CG
|
B:PRO264
|
3.4
|
16.3
|
1.0
|
|
O7
|
A:V5V401
|
3.6
|
13.0
|
0.5
|
|
CB
|
B:THR263
|
3.6
|
15.5
|
1.0
|
|
CE1
|
B:TYR163
|
3.6
|
13.9
|
1.0
|
|
N5
|
A:V5V401
|
3.6
|
13.4
|
0.5
|
|
N5
|
A:V5V401
|
3.6
|
13.8
|
0.5
|
|
P1
|
A:V5V401
|
3.7
|
13.1
|
0.5
|
|
P1
|
A:V5V401
|
3.8
|
13.6
|
0.5
|
|
S
|
A:V5V401
|
4.0
|
13.5
|
0.5
|
|
OG1
|
B:THR263
|
4.0
|
15.3
|
1.0
|
|
N
|
B:PRO264
|
4.0
|
16.3
|
1.0
|
|
N7
|
A:V5V401
|
4.0
|
13.9
|
0.5
|
|
N7
|
A:V5V401
|
4.1
|
13.6
|
0.5
|
|
C14
|
A:V5V401
|
4.2
|
13.1
|
0.5
|
|
C15
|
A:V5V401
|
4.3
|
13.8
|
0.5
|
|
C15
|
A:V5V401
|
4.3
|
13.4
|
0.5
|
|
CA
|
B:THR263
|
4.3
|
15.8
|
1.0
|
|
N
|
B:THR263
|
4.3
|
15.7
|
1.0
|
|
C14
|
A:V5V401
|
4.4
|
13.6
|
0.5
|
|
C
|
B:THR263
|
4.4
|
16.0
|
1.0
|
|
CG2
|
B:THR263
|
4.5
|
15.5
|
1.0
|
|
CG
|
B:TYR163
|
4.6
|
14.0
|
1.0
|
|
O7
|
A:V5V401
|
4.7
|
13.7
|
0.5
|
|
C17
|
A:V5V401
|
4.7
|
13.4
|
0.5
|
|
O
|
B:HOH401
|
4.7
|
28.9
|
1.0
|
|
CB
|
B:PRO264
|
4.7
|
16.4
|
1.0
|
|
C17
|
A:V5V401
|
4.7
|
13.7
|
0.5
|
|
O
|
A:HOH556
|
4.8
|
19.7
|
1.0
|
|
S
|
A:V5V401
|
4.8
|
13.2
|
0.5
|
|
CA
|
B:PRO264
|
4.8
|
16.7
|
1.0
|
|
O6
|
A:V5V401
|
4.9
|
13.1
|
0.5
|
|
O2
|
A:V5V401
|
4.9
|
13.6
|
0.5
|
|
CZ
|
B:TYR163
|
4.9
|
13.8
|
1.0
|
|
O2
|
A:V5V401
|
5.0
|
13.1
|
0.5
|
|
NH2
|
A:ARG238
|
5.0
|
20.5
|
0.5
|
|
NH1
|
A:ARG238
|
5.0
|
20.1
|
0.5
|
|
Fluorine binding site 4 out
of 4 in 6xf3
Go back to
Fluorine Binding Sites List in 6xf3
Fluorine binding site 4 out
of 4 in the Crystal Structure of Sting in Complex with E7766
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Sting in Complex with E7766 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.7
occ:0.50
|
F
|
A:V5V401
|
0.0
|
13.7
|
0.5
|
|
F
|
A:V5V401
|
0.0
|
13.3
|
0.5
|
|
C10
|
A:V5V401
|
1.3
|
13.2
|
0.5
|
|
C10
|
A:V5V401
|
1.4
|
13.6
|
0.5
|
|
C13
|
A:V5V401
|
2.3
|
13.2
|
0.5
|
|
C13
|
A:V5V401
|
2.3
|
13.6
|
0.5
|
|
C11
|
A:V5V401
|
2.3
|
13.2
|
0.5
|
|
C11
|
A:V5V401
|
2.4
|
13.6
|
0.5
|
|
O5
|
A:V5V401
|
2.7
|
13.6
|
0.5
|
|
C12
|
A:V5V401
|
2.7
|
13.2
|
0.5
|
|
O5
|
A:V5V401
|
2.7
|
13.2
|
0.5
|
|
C12
|
A:V5V401
|
2.8
|
13.6
|
0.5
|
|
O4
|
A:V5V401
|
3.0
|
13.1
|
0.5
|
|
O4
|
A:V5V401
|
3.0
|
13.5
|
0.5
|
|
CD
|
B:PRO264
|
3.2
|
16.2
|
1.0
|
|
O
|
B:HOH417
|
3.3
|
14.2
|
1.0
|
|
CD1
|
B:TYR163
|
3.3
|
13.9
|
1.0
|
|
CG
|
B:PRO264
|
3.4
|
16.3
|
1.0
|
|
O7
|
A:V5V401
|
3.6
|
13.0
|
0.5
|
|
N5
|
A:V5V401
|
3.6
|
13.4
|
0.5
|
|
N5
|
A:V5V401
|
3.6
|
13.8
|
0.5
|
|
CE1
|
B:TYR163
|
3.6
|
13.9
|
1.0
|
|
CB
|
B:THR263
|
3.6
|
15.5
|
1.0
|
|
P1
|
A:V5V401
|
3.7
|
13.1
|
0.5
|
|
P1
|
A:V5V401
|
3.8
|
13.6
|
0.5
|
|
S
|
A:V5V401
|
4.0
|
13.5
|
0.5
|
|
N
|
B:PRO264
|
4.0
|
16.3
|
1.0
|
|
OG1
|
B:THR263
|
4.0
|
15.3
|
1.0
|
|
N7
|
A:V5V401
|
4.0
|
13.9
|
0.5
|
|
N7
|
A:V5V401
|
4.1
|
13.6
|
0.5
|
|
C14
|
A:V5V401
|
4.2
|
13.1
|
0.5
|
|
C15
|
A:V5V401
|
4.2
|
13.8
|
0.5
|
|
C15
|
A:V5V401
|
4.3
|
13.4
|
0.5
|
|
C14
|
A:V5V401
|
4.3
|
13.6
|
0.5
|
|
CA
|
B:THR263
|
4.3
|
15.8
|
1.0
|
|
N
|
B:THR263
|
4.3
|
15.7
|
1.0
|
|
C
|
B:THR263
|
4.5
|
16.0
|
1.0
|
|
CG
|
B:TYR163
|
4.6
|
14.0
|
1.0
|
|
CG2
|
B:THR263
|
4.6
|
15.5
|
1.0
|
|
C17
|
A:V5V401
|
4.7
|
13.4
|
0.5
|
|
O7
|
A:V5V401
|
4.7
|
13.7
|
0.5
|
|
O
|
B:HOH401
|
4.7
|
28.9
|
1.0
|
|
C17
|
A:V5V401
|
4.7
|
13.7
|
0.5
|
|
CB
|
B:PRO264
|
4.7
|
16.4
|
1.0
|
|
O
|
A:HOH556
|
4.8
|
19.7
|
1.0
|
|
S
|
A:V5V401
|
4.8
|
13.2
|
0.5
|
|
O6
|
A:V5V401
|
4.8
|
13.1
|
0.5
|
|
CA
|
B:PRO264
|
4.9
|
16.7
|
1.0
|
|
O2
|
A:V5V401
|
4.9
|
13.6
|
0.5
|
|
O2
|
A:V5V401
|
4.9
|
13.1
|
0.5
|
|
CZ
|
B:TYR163
|
4.9
|
13.8
|
1.0
|
|
NH2
|
A:ARG238
|
5.0
|
20.5
|
0.5
|
|
NH1
|
A:ARG238
|
5.0
|
20.1
|
0.5
|
|
Reference:
D.S.Kim,
A.Endo,
F.G.Fang,
K.C.Huang,
X.Bao,
H.W.Choi,
U.Majumder,
Y.Y.Shen,
S.Mathieu,
X.Zhu,
K.Sanders,
T.Noland,
M.H.Hao,
Y.Chen,
J.Y.Wang,
S.Yasui,
K.Tendyke,
J.Wu,
C.Ingersoll,
K.A.Loiacono,
J.E.Hutz,
N.Sarwar.
E7766, A Macrocycle-Bridged Stimulator of Interferon Genes (Sting) Agonist with Potent Pan-Genotypic Activity. Chemmedchem 2021.
ISSN: ESSN 1860-7187
PubMed: 33522135
DOI: 10.1002/CMDC.202100068
Page generated: Fri Aug 2 04:05:38 2024
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