Fluorine in PDB 7p4u: Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole
Protein crystallography data
The structure of Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole, PDB code: 7p4u
was solved by
S.Schmelz,
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
60.16 /
2.74
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.319,
120.319,
115.201,
90,
90,
120
|
R / Rfree (%)
|
24.6 /
27.5
|
Other elements in 7p4u:
The structure of Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole
(pdb code 7p4u). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole, PDB code: 7p4u:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7p4u
Go back to
Fluorine Binding Sites List in 7p4u
Fluorine binding site 1 out
of 3 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole
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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:56.8
occ:1.00
|
F08
|
A:5N9401
|
0.0
|
56.8
|
1.0
|
C07
|
A:5N9401
|
1.4
|
54.9
|
1.0
|
F10
|
A:5N9401
|
2.2
|
58.3
|
1.0
|
F09
|
A:5N9401
|
2.2
|
60.3
|
1.0
|
C06
|
A:5N9401
|
2.4
|
53.6
|
1.0
|
HZ
|
A:PHE221
|
2.8
|
66.9
|
1.0
|
HB2
|
A:ALA102
|
2.8
|
68.6
|
1.0
|
HD13
|
A:ILE149
|
2.8
|
58.4
|
1.0
|
HD11
|
A:ILE149
|
2.9
|
58.4
|
1.0
|
N01
|
A:5N9401
|
3.0
|
62.1
|
1.0
|
CD1
|
A:ILE149
|
3.2
|
47.1
|
1.0
|
HB1
|
A:ALA102
|
3.3
|
68.6
|
1.0
|
C05
|
A:5N9401
|
3.4
|
60.9
|
1.0
|
HG2
|
A:PRO129
|
3.5
|
60.4
|
1.0
|
HD12
|
A:ILE149
|
3.5
|
58.4
|
1.0
|
CB
|
A:ALA102
|
3.5
|
55.6
|
1.0
|
H051
|
A:5N9401
|
3.5
|
75.0
|
1.0
|
CZ
|
A:PHE221
|
3.6
|
54.2
|
1.0
|
HG3
|
A:PRO238
|
3.6
|
68.0
|
1.0
|
HB3
|
A:ALA102
|
4.1
|
68.6
|
1.0
|
C02
|
A:5N9401
|
4.2
|
70.3
|
1.0
|
HE1
|
A:PHE221
|
4.2
|
65.4
|
1.0
|
HA
|
A:ALA102
|
4.3
|
56.1
|
1.0
|
HD3
|
A:PRO238
|
4.3
|
68.2
|
1.0
|
CG
|
A:PRO129
|
4.3
|
48.8
|
1.0
|
HE2
|
A:PHE221
|
4.3
|
62.9
|
1.0
|
CE1
|
A:PHE221
|
4.4
|
53.0
|
1.0
|
HD21
|
A:LEU208
|
4.4
|
101.8
|
1.0
|
CE2
|
A:PHE221
|
4.4
|
50.8
|
1.0
|
HB2
|
A:ALA168
|
4.5
|
54.3
|
1.0
|
HG3
|
A:PRO129
|
4.5
|
60.4
|
1.0
|
CG
|
A:PRO238
|
4.5
|
55.1
|
1.0
|
CA
|
A:ALA102
|
4.5
|
45.2
|
1.0
|
HD12
|
A:LEU197
|
4.5
|
85.0
|
1.0
|
C04
|
A:5N9401
|
4.6
|
65.6
|
1.0
|
CG1
|
A:ILE149
|
4.7
|
41.6
|
1.0
|
HG12
|
A:ILE149
|
4.8
|
51.9
|
1.0
|
HB3
|
A:PRO129
|
4.8
|
59.6
|
1.0
|
HB2
|
A:PRO129
|
4.8
|
59.6
|
1.0
|
CD
|
A:PRO238
|
4.8
|
55.3
|
1.0
|
H021
|
A:5N9401
|
4.8
|
86.2
|
1.0
|
HG22
|
A:ILE149
|
4.9
|
61.0
|
1.0
|
HA
|
A:ALA237
|
4.9
|
57.7
|
1.0
|
HB1
|
A:ALA168
|
4.9
|
54.3
|
1.0
|
CB
|
A:PRO129
|
4.9
|
48.2
|
1.0
|
C03
|
A:5N9401
|
4.9
|
66.2
|
1.0
|
N
|
A:PRO238
|
4.9
|
48.4
|
1.0
|
HG22
|
A:ILE236
|
5.0
|
65.1
|
1.0
|
O
|
A:ILE236
|
5.0
|
53.6
|
1.0
|
HA
|
A:PRO238
|
5.0
|
54.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7p4u
Go back to
Fluorine Binding Sites List in 7p4u
Fluorine binding site 2 out
of 3 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole
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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:60.3
occ:1.00
|
F09
|
A:5N9401
|
0.0
|
60.3
|
1.0
|
C07
|
A:5N9401
|
1.4
|
54.9
|
1.0
|
F08
|
A:5N9401
|
2.2
|
56.8
|
1.0
|
F10
|
A:5N9401
|
2.2
|
58.3
|
1.0
|
C06
|
A:5N9401
|
2.4
|
53.6
|
1.0
|
N01
|
A:5N9401
|
2.9
|
62.1
|
1.0
|
HG22
|
A:ILE236
|
2.9
|
65.1
|
1.0
|
HB1
|
A:ALA168
|
3.0
|
54.3
|
1.0
|
HB2
|
A:ALA168
|
3.2
|
54.3
|
1.0
|
HA
|
A:ALA237
|
3.3
|
57.7
|
1.0
|
O
|
A:ILE236
|
3.4
|
53.6
|
1.0
|
C
|
A:ALA237
|
3.5
|
48.8
|
1.0
|
C05
|
A:5N9401
|
3.5
|
60.9
|
1.0
|
CB
|
A:ALA168
|
3.6
|
43.7
|
1.0
|
HZ
|
A:PHE221
|
3.6
|
66.9
|
1.0
|
C
|
A:ILE236
|
3.6
|
46.3
|
1.0
|
HD3
|
A:PRO238
|
3.6
|
68.2
|
1.0
|
CA
|
A:ALA237
|
3.7
|
46.6
|
1.0
|
N
|
A:PRO238
|
3.7
|
48.4
|
1.0
|
N
|
A:ALA237
|
3.7
|
42.7
|
1.0
|
H051
|
A:5N9401
|
3.7
|
75.0
|
1.0
|
CG2
|
A:ILE236
|
3.7
|
52.7
|
1.0
|
HG3
|
A:PRO238
|
3.8
|
68.0
|
1.0
|
O
|
A:ALA237
|
3.8
|
50.1
|
1.0
|
HG21
|
A:ILE236
|
3.8
|
65.1
|
1.0
|
HE1
|
A:PHE221
|
3.8
|
65.4
|
1.0
|
HA
|
A:PRO238
|
4.0
|
54.1
|
1.0
|
HB
|
A:ILE236
|
4.0
|
51.1
|
1.0
|
CD
|
A:PRO238
|
4.1
|
55.3
|
1.0
|
CZ
|
A:PHE221
|
4.1
|
54.2
|
1.0
|
C02
|
A:5N9401
|
4.1
|
70.3
|
1.0
|
H
|
A:ALA237
|
4.1
|
53.2
|
1.0
|
HB3
|
A:ALA168
|
4.2
|
54.3
|
1.0
|
CE1
|
A:PHE221
|
4.2
|
53.0
|
1.0
|
CB
|
A:ILE236
|
4.3
|
41.0
|
1.0
|
CA
|
A:PRO238
|
4.4
|
43.5
|
1.0
|
CG
|
A:PRO238
|
4.4
|
55.1
|
1.0
|
HA
|
A:ALA168
|
4.5
|
54.8
|
1.0
|
HG23
|
A:ILE236
|
4.5
|
65.1
|
1.0
|
CA
|
A:ILE236
|
4.6
|
44.5
|
1.0
|
C04
|
A:5N9401
|
4.6
|
65.6
|
1.0
|
H021
|
A:5N9401
|
4.7
|
86.2
|
1.0
|
CA
|
A:ALA168
|
4.7
|
44.1
|
1.0
|
HB2
|
A:ALA102
|
4.7
|
68.6
|
1.0
|
HD13
|
A:ILE149
|
4.8
|
58.4
|
1.0
|
H
|
A:PHE169
|
4.8
|
58.7
|
1.0
|
HB1
|
A:ALA102
|
4.8
|
68.6
|
1.0
|
O
|
A:HOH505
|
4.8
|
55.2
|
1.0
|
C03
|
A:5N9401
|
4.9
|
66.2
|
1.0
|
HD11
|
A:ILE149
|
4.9
|
58.4
|
1.0
|
CB
|
A:PRO238
|
4.9
|
54.9
|
1.0
|
HD2
|
A:PRO238
|
5.0
|
68.2
|
1.0
|
HA
|
A:ILE236
|
5.0
|
55.3
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7p4u
Go back to
Fluorine Binding Sites List in 7p4u
Fluorine binding site 3 out
of 3 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole
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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with 3-Pyridin-4-Yl-2,4-Dihydro-Indeno[1,2-.C.]Pyrazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:58.3
occ:1.00
|
F10
|
A:5N9401
|
0.0
|
58.3
|
1.0
|
C07
|
A:5N9401
|
1.4
|
54.9
|
1.0
|
F08
|
A:5N9401
|
2.2
|
56.8
|
1.0
|
F09
|
A:5N9401
|
2.2
|
60.3
|
1.0
|
H051
|
A:5N9401
|
2.3
|
75.0
|
1.0
|
C06
|
A:5N9401
|
2.4
|
53.6
|
1.0
|
HB2
|
A:ALA168
|
2.4
|
54.3
|
1.0
|
C05
|
A:5N9401
|
2.7
|
60.9
|
1.0
|
HD13
|
A:ILE149
|
3.2
|
58.4
|
1.0
|
CB
|
A:ALA168
|
3.2
|
43.7
|
1.0
|
HB1
|
A:ALA168
|
3.3
|
54.3
|
1.0
|
HD12
|
A:ILE149
|
3.5
|
58.4
|
1.0
|
HG1
|
A:THR265
|
3.5
|
75.7
|
1.0
|
N01
|
A:5N9401
|
3.6
|
62.1
|
1.0
|
HB3
|
A:ALA168
|
3.6
|
54.3
|
1.0
|
HB1
|
A:ALA102
|
3.6
|
68.6
|
1.0
|
CD1
|
A:ILE149
|
3.7
|
47.1
|
1.0
|
HD11
|
A:ILE149
|
3.9
|
58.4
|
1.0
|
C04
|
A:5N9401
|
4.1
|
65.6
|
1.0
|
HB2
|
A:ALA102
|
4.1
|
68.6
|
1.0
|
HA
|
A:PRO238
|
4.1
|
54.1
|
1.0
|
HG3
|
A:PRO238
|
4.3
|
68.0
|
1.0
|
HG21
|
A:THR265
|
4.3
|
81.5
|
1.0
|
HG22
|
A:ILE236
|
4.3
|
65.1
|
1.0
|
CB
|
A:ALA102
|
4.3
|
55.6
|
1.0
|
OG1
|
A:THR265
|
4.3
|
61.5
|
1.0
|
HG23
|
A:THR166
|
4.4
|
88.9
|
1.0
|
HG22
|
A:ILE149
|
4.4
|
61.0
|
1.0
|
HB
|
A:THR265
|
4.4
|
75.6
|
1.0
|
CA
|
A:ALA168
|
4.4
|
44.1
|
1.0
|
HA
|
A:ALA168
|
4.4
|
54.8
|
1.0
|
HG21
|
A:THR166
|
4.7
|
88.9
|
1.0
|
C02
|
A:5N9401
|
4.7
|
70.3
|
1.0
|
HG21
|
A:ILE236
|
4.7
|
65.1
|
1.0
|
HZ
|
A:PHE221
|
4.8
|
66.9
|
1.0
|
O
|
A:LYS167
|
4.8
|
60.1
|
1.0
|
H111
|
A:5N9401
|
4.8
|
92.1
|
1.0
|
CB
|
A:THR265
|
4.8
|
61.5
|
1.0
|
N
|
A:PRO238
|
4.8
|
48.4
|
1.0
|
CA
|
A:PRO238
|
4.9
|
43.5
|
1.0
|
HB3
|
A:ALA102
|
4.9
|
68.6
|
1.0
|
C03
|
A:5N9401
|
4.9
|
66.2
|
1.0
|
N
|
A:ALA168
|
4.9
|
50.5
|
1.0
|
C
|
A:ALA237
|
4.9
|
48.8
|
1.0
|
O
|
A:ALA237
|
4.9
|
50.1
|
1.0
|
HB3
|
A:PRO238
|
4.9
|
67.8
|
1.0
|
N11
|
A:5N9401
|
4.9
|
75.2
|
1.0
|
CG2
|
A:ILE236
|
5.0
|
52.7
|
1.0
|
CG2
|
A:THR166
|
5.0
|
72.5
|
1.0
|
CG2
|
A:THR265
|
5.0
|
66.4
|
1.0
|
|
Reference:
W.Blankenfeldt,
S.Schmelz.
Divergent Synthesis and Biological Evaluation of 2-(Trifluoromethyl)Pyridines As Virulence-Attenuating Inverse Agonists Targeting Pqsr To Be Published.
Page generated: Fri Aug 2 10:56:04 2024
|