Fluorine in PDB 7hgn: Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006, PDB code: 7hgn
was solved by
T.Vantieghem,
E.Osipov,
D.Fearon,
A.Douangamath,
F.Von Delft,
S.Strelkov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.55 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.31,
41.92,
158.03,
90,
90,
90
|
R / Rfree (%)
|
20 /
24.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
(pdb code 7hgn). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006, PDB code: 7hgn:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 7hgn
Go back to
Fluorine Binding Sites List in 7hgn
Fluorine binding site 1 out
of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F103
b:37.7
occ:0.84
|
F
|
B:NX7103
|
0.0
|
37.7
|
0.8
|
C
|
B:NX7103
|
1.3
|
35.8
|
0.8
|
C5
|
B:NX7103
|
2.3
|
31.0
|
0.8
|
C1
|
B:NX7103
|
2.4
|
40.3
|
0.8
|
C6
|
B:NX7103
|
2.8
|
28.9
|
0.8
|
CB
|
B:GLU49
|
3.2
|
39.5
|
1.0
|
CD1
|
B:PHE44
|
3.3
|
26.3
|
1.0
|
N
|
B:NX7103
|
3.3
|
27.9
|
0.8
|
CE1
|
B:PHE44
|
3.3
|
33.5
|
1.0
|
C10
|
B:NX7103
|
3.5
|
27.8
|
0.8
|
O
|
B:NX7103
|
3.5
|
34.1
|
0.8
|
C4
|
B:NX7103
|
3.6
|
37.6
|
0.8
|
C2
|
B:NX7103
|
3.6
|
39.1
|
0.8
|
O
|
B:THR50
|
3.9
|
33.8
|
1.0
|
N
|
B:THR50
|
4.1
|
31.9
|
1.0
|
C3
|
B:NX7103
|
4.1
|
37.1
|
0.8
|
CG
|
B:PHE44
|
4.1
|
22.4
|
1.0
|
C
|
B:THR50
|
4.1
|
34.8
|
1.0
|
C
|
B:GLU49
|
4.1
|
32.9
|
1.0
|
CG
|
B:GLU49
|
4.2
|
41.9
|
1.0
|
CZ
|
B:PHE44
|
4.2
|
28.5
|
1.0
|
C9
|
B:NX7103
|
4.3
|
27.0
|
0.8
|
C7
|
B:NX7103
|
4.4
|
28.7
|
0.8
|
CE
|
B:MET15
|
4.4
|
51.0
|
1.0
|
CB
|
B:ALA51
|
4.4
|
34.1
|
1.0
|
CA
|
B:GLU49
|
4.4
|
32.9
|
1.0
|
SD
|
B:MET15
|
4.4
|
40.8
|
1.0
|
OE1
|
B:GLU49
|
4.6
|
50.4
|
1.0
|
CA
|
B:THR50
|
4.6
|
33.3
|
1.0
|
O
|
B:GLU49
|
4.6
|
32.2
|
1.0
|
F1
|
B:NX7103
|
4.7
|
37.1
|
0.8
|
CD
|
B:GLU49
|
4.7
|
46.4
|
1.0
|
N
|
B:ALA51
|
4.7
|
33.0
|
1.0
|
CB
|
B:PHE44
|
4.8
|
22.2
|
1.0
|
CD2
|
B:PHE44
|
4.8
|
22.6
|
1.0
|
CE2
|
B:PHE44
|
4.8
|
29.1
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 7hgn
Go back to
Fluorine Binding Sites List in 7hgn
Fluorine binding site 2 out
of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F103
b:37.1
occ:0.84
|
F1
|
B:NX7103
|
0.0
|
37.1
|
0.8
|
C4
|
B:NX7103
|
1.4
|
37.6
|
0.8
|
C5
|
B:NX7103
|
2.3
|
31.0
|
0.8
|
C3
|
B:NX7103
|
2.4
|
37.1
|
0.8
|
C6
|
B:NX7103
|
2.8
|
28.9
|
0.8
|
O
|
A:ASP30
|
3.0
|
29.6
|
1.0
|
O
|
B:NX7103
|
3.2
|
34.1
|
0.8
|
O
|
B:HOH218
|
3.3
|
38.2
|
1.0
|
N
|
B:NX7103
|
3.5
|
27.9
|
0.8
|
CB
|
A:ASP30
|
3.5
|
30.0
|
1.0
|
C
|
B:NX7103
|
3.6
|
35.8
|
0.8
|
C2
|
B:NX7103
|
3.6
|
39.1
|
0.8
|
C
|
A:ASP30
|
3.7
|
22.5
|
1.0
|
OH
|
B:TYR18
|
3.8
|
34.4
|
1.0
|
C10
|
B:NX7103
|
3.9
|
27.8
|
0.8
|
C1
|
B:NX7103
|
4.1
|
40.3
|
0.8
|
CE1
|
B:TYR18
|
4.2
|
35.1
|
1.0
|
CZ
|
B:TYR18
|
4.2
|
34.9
|
1.0
|
OE2
|
B:GLU49
|
4.2
|
45.4
|
1.0
|
CA
|
A:ASP30
|
4.2
|
28.3
|
1.0
|
CD
|
B:GLU49
|
4.4
|
46.4
|
1.0
|
CG
|
B:GLU49
|
4.5
|
41.9
|
1.0
|
N
|
A:GLY31
|
4.5
|
25.2
|
1.0
|
C7
|
B:NX7103
|
4.6
|
28.7
|
0.8
|
F
|
B:NX7103
|
4.7
|
37.7
|
0.8
|
N
|
A:ASP30
|
4.7
|
28.7
|
1.0
|
CA
|
A:GLY31
|
4.8
|
27.1
|
1.0
|
CG
|
A:ASP30
|
4.8
|
31.4
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 7hgn
Go back to
Fluorine Binding Sites List in 7hgn
Fluorine binding site 3 out
of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F102
b:42.2
occ:0.54
|
F
|
C:NX7102
|
0.0
|
42.2
|
0.5
|
C
|
C:NX7102
|
1.4
|
39.4
|
0.5
|
C1
|
C:NX7102
|
2.4
|
42.0
|
0.5
|
C5
|
C:NX7102
|
2.4
|
38.6
|
0.5
|
C6
|
C:NX7102
|
2.9
|
38.4
|
0.5
|
OE1
|
C:GLU49
|
3.2
|
65.5
|
1.0
|
OH
|
C:TYR18
|
3.2
|
43.6
|
1.0
|
N
|
C:NX7102
|
3.4
|
36.5
|
0.5
|
C7
|
C:NX7102
|
3.5
|
34.0
|
0.5
|
C4
|
C:NX7102
|
3.6
|
42.0
|
0.5
|
C2
|
C:NX7102
|
3.6
|
39.8
|
0.5
|
CZ
|
C:TYR18
|
3.7
|
32.9
|
1.0
|
O
|
C:NX7102
|
3.7
|
31.9
|
0.5
|
CE2
|
C:TYR18
|
3.7
|
33.9
|
1.0
|
CD
|
C:GLU49
|
4.1
|
57.9
|
1.0
|
C3
|
C:NX7102
|
4.1
|
39.4
|
0.5
|
OE2
|
C:GLU49
|
4.3
|
65.7
|
1.0
|
C10
|
C:NX7102
|
4.5
|
34.5
|
0.5
|
CE1
|
C:TYR18
|
4.6
|
30.0
|
1.0
|
F1
|
C:NX7102
|
4.7
|
46.6
|
0.5
|
CD2
|
C:TYR18
|
4.7
|
25.8
|
1.0
|
O
|
C:HOH222
|
4.9
|
43.0
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 7hgn
Go back to
Fluorine Binding Sites List in 7hgn
Fluorine binding site 4 out
of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Hrp-2 Pwwp Domain in Complex with Z54226006 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F102
b:46.6
occ:0.54
|
F1
|
C:NX7102
|
0.0
|
46.6
|
0.5
|
C4
|
C:NX7102
|
1.3
|
42.0
|
0.5
|
C3
|
C:NX7102
|
2.3
|
39.4
|
0.5
|
C5
|
C:NX7102
|
2.3
|
38.6
|
0.5
|
C6
|
C:NX7102
|
2.8
|
38.4
|
0.5
|
CD2
|
C:PHE44
|
3.0
|
28.1
|
1.0
|
O
|
C:NX7102
|
3.1
|
31.9
|
0.5
|
CE2
|
C:PHE44
|
3.2
|
30.1
|
1.0
|
CB
|
C:GLU49
|
3.3
|
37.2
|
1.0
|
N
|
C:NX7102
|
3.5
|
36.5
|
0.5
|
O
|
C:THR50
|
3.5
|
35.5
|
1.0
|
C
|
C:NX7102
|
3.6
|
39.4
|
0.5
|
C2
|
C:NX7102
|
3.6
|
39.8
|
0.5
|
C
|
C:GLU49
|
3.8
|
40.1
|
1.0
|
N
|
C:THR50
|
3.9
|
34.4
|
1.0
|
C
|
C:THR50
|
3.9
|
31.6
|
1.0
|
OE1
|
C:GLU49
|
3.9
|
65.5
|
1.0
|
C7
|
C:NX7102
|
3.9
|
34.0
|
0.5
|
CG
|
C:PHE44
|
4.0
|
27.6
|
1.0
|
C1
|
C:NX7102
|
4.1
|
42.0
|
0.5
|
O
|
C:GLU49
|
4.2
|
35.1
|
1.0
|
CB
|
C:ALA51
|
4.2
|
33.8
|
1.0
|
CA
|
C:GLU49
|
4.2
|
38.0
|
1.0
|
CZ
|
C:PHE44
|
4.3
|
30.9
|
1.0
|
CA
|
C:THR50
|
4.3
|
36.1
|
1.0
|
SD
|
C:MET15
|
4.4
|
43.5
|
1.0
|
N
|
C:ALA51
|
4.5
|
33.9
|
1.0
|
C8
|
C:NX7102
|
4.5
|
32.2
|
0.5
|
CG
|
C:GLU49
|
4.6
|
48.6
|
1.0
|
C10
|
C:NX7102
|
4.6
|
34.5
|
0.5
|
CD
|
C:GLU49
|
4.6
|
57.9
|
1.0
|
CB
|
C:PHE44
|
4.6
|
26.0
|
1.0
|
F
|
C:NX7102
|
4.7
|
42.2
|
0.5
|
CE
|
C:MET15
|
4.9
|
46.4
|
1.0
|
CD1
|
C:PHE44
|
4.9
|
25.1
|
1.0
|
CA
|
C:ALA51
|
4.9
|
32.1
|
1.0
|
|
Reference:
T.Vantieghem,
N.A.Aslam,
E.M.Osipov,
M.Akele,
S.Van Belle,
S.Beelen,
M.Drexler,
T.Paulovcakova,
V.Lux,
D.Fearon,
A.Douangamath,
F.Von Delft,
F.Christ,
V.Veverka,
P.Verwilst,
A.Van Aerschot,
Z.Debyser,
S.V.Strelkov.
Rational Fragment-Based Design of Compounds Targeting the Pwwp Domain of the Hrp Family. Eur.J.Med.Chem. V. 280 16960 2024.
ISSN: ISSN 0223-5234
PubMed: 39461037
DOI: 10.1016/J.EJMECH.2024.116960
Page generated: Wed Nov 13 08:11:41 2024
|