Fluorine in PDB 8ahf: Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
Enzymatic activity of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
All present enzymatic activity of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery:
5.1.3.14;
Protein crystallography data
The structure of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery, PDB code: 8ahf
was solved by
L.M.Baker,
J.B.Murray,
R.E.Hubbard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
85.17 /
2.27
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.315,
109.315,
135.866,
90,
90,
90
|
R / Rfree (%)
|
17.7 /
23.8
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
(pdb code 8ahf). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery, PDB code: 8ahf:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 8ahf
Go back to
Fluorine Binding Sites List in 8ahf
Fluorine binding site 1 out
of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:62.8
occ:1.00
|
F1
|
A:M3U401
|
0.0
|
62.8
|
1.0
|
C6
|
A:M3U401
|
1.3
|
59.7
|
1.0
|
H9
|
A:M3U401
|
1.9
|
60.1
|
1.0
|
F2
|
A:M3U401
|
2.1
|
56.0
|
1.0
|
O2
|
A:M3U401
|
2.3
|
62.8
|
1.0
|
HA
|
A:VAL289
|
2.3
|
37.2
|
1.0
|
HB2
|
A:GLU292
|
2.6
|
45.1
|
1.0
|
HB2
|
A:ALA293
|
2.9
|
40.4
|
1.0
|
H
|
A:ALA293
|
2.9
|
42.8
|
1.0
|
HE2
|
A:PHE272
|
3.0
|
42.0
|
1.0
|
HG23
|
A:VAL289
|
3.1
|
40.5
|
1.0
|
CA
|
A:VAL289
|
3.2
|
34.5
|
1.0
|
HG11
|
A:VAL289
|
3.3
|
41.0
|
1.0
|
N
|
A:ALA293
|
3.3
|
43.1
|
1.0
|
CB
|
A:GLU292
|
3.5
|
45.3
|
1.0
|
HB3
|
A:GLU292
|
3.6
|
45.1
|
1.0
|
C5
|
A:M3U401
|
3.6
|
61.7
|
1.0
|
HA
|
A:ALA293
|
3.7
|
42.3
|
1.0
|
CB
|
A:ALA293
|
3.7
|
38.7
|
1.0
|
H8
|
A:M3U401
|
3.7
|
63.4
|
1.0
|
CG2
|
A:VAL289
|
3.8
|
41.0
|
1.0
|
CA
|
A:ALA293
|
3.8
|
44.5
|
1.0
|
CB
|
A:VAL289
|
3.8
|
39.0
|
1.0
|
O
|
A:VAL289
|
3.9
|
42.3
|
1.0
|
O
|
A:GLY288
|
3.9
|
43.5
|
1.0
|
HG22
|
A:VAL289
|
4.0
|
40.4
|
1.0
|
CE2
|
A:PHE272
|
4.0
|
40.4
|
1.0
|
H6
|
A:M3U401
|
4.0
|
63.7
|
1.0
|
N
|
A:VAL289
|
4.0
|
41.4
|
1.0
|
OE1
|
A:GLU292
|
4.0
|
58.7
|
1.0
|
CG1
|
A:VAL289
|
4.0
|
41.9
|
1.0
|
C
|
A:VAL289
|
4.1
|
37.5
|
1.0
|
C
|
A:GLU292
|
4.1
|
40.4
|
1.0
|
H
|
A:GLU292
|
4.1
|
44.1
|
1.0
|
CA
|
A:GLU292
|
4.2
|
41.2
|
1.0
|
HB3
|
A:ALA293
|
4.2
|
40.4
|
1.0
|
C
|
A:GLY288
|
4.2
|
46.1
|
1.0
|
C4
|
A:M3U401
|
4.3
|
65.1
|
1.0
|
HD2
|
A:PHE272
|
4.3
|
44.8
|
1.0
|
HB1
|
A:ALA293
|
4.4
|
40.4
|
1.0
|
CG
|
A:GLU292
|
4.5
|
48.6
|
1.0
|
CD
|
A:GLU292
|
4.5
|
55.0
|
1.0
|
H11
|
A:M3U401
|
4.6
|
64.1
|
1.0
|
N
|
A:GLU292
|
4.6
|
44.5
|
1.0
|
H5
|
A:M3U401
|
4.6
|
64.3
|
1.0
|
CD2
|
A:PHE272
|
4.6
|
47.2
|
1.0
|
H
|
A:VAL289
|
4.6
|
40.7
|
1.0
|
HG12
|
A:VAL289
|
4.6
|
41.0
|
1.0
|
HG21
|
A:VAL289
|
4.6
|
40.4
|
1.0
|
C7
|
A:M3U401
|
4.7
|
66.4
|
1.0
|
HG13
|
A:VAL289
|
4.7
|
41.0
|
1.0
|
HB
|
A:VAL289
|
4.8
|
39.0
|
1.0
|
HD13
|
A:LEU296
|
4.9
|
43.1
|
1.0
|
HD2
|
A:HIS273
|
4.9
|
45.0
|
1.0
|
HZ
|
A:PHE272
|
4.9
|
41.2
|
1.0
|
CZ
|
A:PHE272
|
5.0
|
40.0
|
1.0
|
C3
|
A:M3U401
|
5.0
|
62.5
|
1.0
|
HG3
|
A:GLU292
|
5.0
|
49.2
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 8ahf
Go back to
Fluorine Binding Sites List in 8ahf
Fluorine binding site 2 out
of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:56.0
occ:1.00
|
F2
|
A:M3U401
|
0.0
|
56.0
|
1.0
|
C6
|
A:M3U401
|
1.3
|
59.7
|
1.0
|
H9
|
A:M3U401
|
1.9
|
60.1
|
1.0
|
F1
|
A:M3U401
|
2.1
|
62.8
|
1.0
|
O2
|
A:M3U401
|
2.2
|
62.8
|
1.0
|
HE2
|
A:PHE272
|
2.5
|
42.0
|
1.0
|
H8
|
A:M3U401
|
2.5
|
63.4
|
1.0
|
HD2
|
A:PHE272
|
2.5
|
44.8
|
1.0
|
HD2
|
A:HIS273
|
2.8
|
45.0
|
1.0
|
C5
|
A:M3U401
|
2.8
|
61.7
|
1.0
|
CE2
|
A:PHE272
|
3.1
|
40.4
|
1.0
|
CD2
|
A:PHE272
|
3.1
|
47.2
|
1.0
|
CD2
|
A:HIS273
|
3.5
|
43.6
|
1.0
|
H11
|
A:M3U401
|
3.7
|
64.1
|
1.0
|
HE2
|
A:HIS273
|
3.8
|
45.7
|
0.0
|
C7
|
A:M3U401
|
3.8
|
66.4
|
1.0
|
HB2
|
A:GLU292
|
3.9
|
45.1
|
1.0
|
HA
|
A:HIS273
|
3.9
|
41.7
|
1.0
|
NE2
|
A:HIS273
|
4.0
|
47.3
|
1.0
|
OE1
|
A:GLU292
|
4.0
|
58.7
|
1.0
|
HG23
|
A:VAL289
|
4.0
|
40.5
|
1.0
|
C4
|
A:M3U401
|
4.1
|
65.1
|
1.0
|
H6
|
A:M3U401
|
4.1
|
63.7
|
1.0
|
HB3
|
A:GLU292
|
4.2
|
45.1
|
1.0
|
HA
|
A:VAL289
|
4.2
|
37.2
|
1.0
|
H10
|
A:M3U401
|
4.4
|
64.2
|
1.0
|
HB3
|
A:ALA276
|
4.5
|
42.9
|
1.0
|
CZ
|
A:PHE272
|
4.5
|
40.0
|
1.0
|
CG
|
A:PHE272
|
4.5
|
44.9
|
1.0
|
HB2
|
A:ALA293
|
4.5
|
40.4
|
1.0
|
CB
|
A:GLU292
|
4.5
|
45.3
|
1.0
|
HB2
|
A:ALA276
|
4.5
|
42.9
|
1.0
|
HD23
|
A:LEU182
|
4.6
|
47.2
|
1.0
|
CG
|
A:HIS273
|
4.6
|
45.1
|
1.0
|
H7
|
A:M3U401
|
4.6
|
63.7
|
1.0
|
HD11
|
A:LEU296
|
4.6
|
43.1
|
1.0
|
HB3
|
A:PHE272
|
4.7
|
41.3
|
1.0
|
HA
|
A:ALA293
|
4.7
|
42.3
|
1.0
|
CA
|
A:HIS273
|
4.7
|
40.3
|
1.0
|
N
|
A:HIS273
|
4.8
|
44.3
|
1.0
|
HZ
|
A:PHE272
|
4.8
|
41.2
|
1.0
|
HD13
|
A:LEU296
|
4.8
|
43.1
|
1.0
|
CB
|
A:ALA276
|
4.8
|
45.1
|
1.0
|
HB1
|
A:ALA276
|
4.8
|
42.9
|
1.0
|
H
|
A:ALA293
|
4.9
|
42.8
|
1.0
|
CG2
|
A:VAL289
|
4.9
|
41.0
|
1.0
|
N2
|
A:M3U401
|
4.9
|
62.1
|
1.0
|
HG22
|
A:VAL289
|
4.9
|
40.4
|
1.0
|
HG11
|
A:VAL289
|
4.9
|
41.0
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 8ahf
Go back to
Fluorine Binding Sites List in 8ahf
Fluorine binding site 3 out
of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:53.2
occ:1.00
|
F1
|
B:M3U401
|
0.0
|
53.2
|
1.0
|
C6
|
B:M3U401
|
1.3
|
57.6
|
1.0
|
H9
|
B:M3U401
|
1.9
|
55.9
|
1.0
|
F2
|
B:M3U401
|
2.2
|
60.2
|
1.0
|
O2
|
B:M3U401
|
2.2
|
51.4
|
1.0
|
HA
|
B:VAL289
|
2.4
|
40.7
|
1.0
|
HB2
|
B:GLU292
|
2.5
|
42.2
|
1.0
|
HB2
|
B:ALA293
|
3.0
|
44.2
|
1.0
|
HG11
|
B:VAL289
|
3.1
|
41.6
|
1.0
|
HE2
|
B:PHE272
|
3.2
|
46.5
|
1.0
|
H
|
B:ALA293
|
3.2
|
42.6
|
1.0
|
HG23
|
B:VAL289
|
3.3
|
43.5
|
1.0
|
CB
|
B:GLU292
|
3.3
|
42.3
|
1.0
|
CA
|
B:VAL289
|
3.3
|
39.6
|
1.0
|
HB3
|
B:GLU292
|
3.4
|
42.1
|
1.0
|
N
|
B:ALA293
|
3.4
|
41.1
|
1.0
|
C5
|
B:M3U401
|
3.5
|
47.9
|
1.0
|
HA
|
B:ALA293
|
3.6
|
41.9
|
1.0
|
H8
|
B:M3U401
|
3.7
|
49.6
|
1.0
|
CB
|
B:ALA293
|
3.7
|
45.1
|
1.0
|
CA
|
B:ALA293
|
3.8
|
42.3
|
1.0
|
O
|
B:VAL289
|
3.8
|
43.5
|
1.0
|
CB
|
B:VAL289
|
3.9
|
41.2
|
1.0
|
CG1
|
B:VAL289
|
3.9
|
41.8
|
1.0
|
CG2
|
B:VAL289
|
3.9
|
44.5
|
1.0
|
H6
|
B:M3U401
|
3.9
|
51.2
|
1.0
|
C
|
B:GLU292
|
4.0
|
46.1
|
1.0
|
O
|
B:GLY288
|
4.0
|
45.2
|
1.0
|
HG22
|
B:VAL289
|
4.0
|
43.5
|
1.0
|
OE1
|
B:GLU292
|
4.0
|
46.7
|
1.0
|
CE2
|
B:PHE272
|
4.1
|
46.1
|
1.0
|
C
|
B:VAL289
|
4.1
|
41.7
|
1.0
|
H
|
B:GLU292
|
4.1
|
46.0
|
1.0
|
CA
|
B:GLU292
|
4.1
|
45.2
|
1.0
|
HB3
|
B:ALA293
|
4.1
|
44.2
|
1.0
|
N
|
B:VAL289
|
4.2
|
41.8
|
1.0
|
C4
|
B:M3U401
|
4.3
|
51.6
|
1.0
|
HG13
|
B:VAL289
|
4.3
|
41.6
|
1.0
|
CG
|
B:GLU292
|
4.4
|
38.6
|
1.0
|
HD2
|
B:PHE272
|
4.4
|
45.9
|
1.0
|
CD
|
B:GLU292
|
4.4
|
41.8
|
1.0
|
C
|
B:GLY288
|
4.5
|
41.7
|
1.0
|
HB1
|
B:ALA293
|
4.5
|
44.2
|
1.0
|
H5
|
B:M3U401
|
4.5
|
53.4
|
1.0
|
H11
|
B:M3U401
|
4.5
|
48.9
|
1.0
|
N
|
B:GLU292
|
4.6
|
48.1
|
1.0
|
C7
|
B:M3U401
|
4.6
|
49.3
|
1.0
|
HG12
|
B:VAL289
|
4.6
|
41.6
|
1.0
|
HD2
|
B:HIS273
|
4.7
|
44.5
|
1.0
|
CD2
|
B:PHE272
|
4.7
|
46.5
|
1.0
|
HG3
|
B:GLU292
|
4.8
|
40.2
|
1.0
|
HG21
|
B:VAL289
|
4.8
|
43.5
|
1.0
|
O
|
B:GLU292
|
4.8
|
52.4
|
1.0
|
HB
|
B:VAL289
|
4.8
|
41.6
|
1.0
|
H
|
B:VAL289
|
4.8
|
41.3
|
1.0
|
C3
|
B:M3U401
|
4.9
|
53.7
|
1.0
|
HZ
|
B:PHE272
|
5.0
|
46.0
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 8ahf
Go back to
Fluorine Binding Sites List in 8ahf
Fluorine binding site 4 out
of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F401
b:60.2
occ:1.00
|
F2
|
B:M3U401
|
0.0
|
60.2
|
1.0
|
C6
|
B:M3U401
|
1.4
|
57.6
|
1.0
|
H9
|
B:M3U401
|
1.9
|
55.9
|
1.0
|
F1
|
B:M3U401
|
2.2
|
53.2
|
1.0
|
O2
|
B:M3U401
|
2.3
|
51.4
|
1.0
|
H8
|
B:M3U401
|
2.4
|
49.6
|
1.0
|
HD2
|
B:HIS273
|
2.6
|
44.5
|
1.0
|
C5
|
B:M3U401
|
2.8
|
47.9
|
1.0
|
HD2
|
B:PHE272
|
2.8
|
45.9
|
1.0
|
HE2
|
B:PHE272
|
2.8
|
46.5
|
1.0
|
CD2
|
B:HIS273
|
3.4
|
43.8
|
1.0
|
CE2
|
B:PHE272
|
3.5
|
46.1
|
1.0
|
CD2
|
B:PHE272
|
3.5
|
46.5
|
1.0
|
HE2
|
B:HIS273
|
3.5
|
46.1
|
0.0
|
H11
|
B:M3U401
|
3.7
|
48.9
|
1.0
|
HB2
|
B:GLU292
|
3.8
|
42.2
|
1.0
|
NE2
|
B:HIS273
|
3.8
|
48.6
|
1.0
|
OE1
|
B:GLU292
|
3.8
|
46.7
|
1.0
|
C7
|
B:M3U401
|
3.8
|
49.3
|
1.0
|
H6
|
B:M3U401
|
3.9
|
51.2
|
1.0
|
HB3
|
B:GLU292
|
3.9
|
42.1
|
1.0
|
C4
|
B:M3U401
|
4.0
|
51.6
|
1.0
|
HA
|
B:HIS273
|
4.0
|
41.6
|
1.0
|
HG23
|
B:VAL289
|
4.3
|
43.5
|
1.0
|
CB
|
B:GLU292
|
4.3
|
42.3
|
1.0
|
HA
|
B:VAL289
|
4.3
|
40.7
|
1.0
|
H10
|
B:M3U401
|
4.4
|
48.9
|
1.0
|
HD23
|
B:LEU182
|
4.4
|
43.3
|
1.0
|
H7
|
B:M3U401
|
4.5
|
51.2
|
1.0
|
HB2
|
B:ALA293
|
4.5
|
44.2
|
1.0
|
CG
|
B:HIS273
|
4.6
|
41.3
|
1.0
|
HA
|
B:ALA293
|
4.7
|
41.9
|
1.0
|
HD11
|
B:LEU296
|
4.7
|
41.8
|
1.0
|
HB3
|
B:ALA276
|
4.7
|
45.5
|
1.0
|
CD
|
B:GLU292
|
4.8
|
41.8
|
1.0
|
CG
|
B:PHE272
|
4.8
|
44.5
|
1.0
|
CZ
|
B:PHE272
|
4.8
|
47.9
|
1.0
|
N2
|
B:M3U401
|
4.8
|
49.0
|
1.0
|
HB3
|
B:PHE272
|
4.9
|
44.5
|
1.0
|
CA
|
B:HIS273
|
4.9
|
40.1
|
1.0
|
HB2
|
B:ALA276
|
4.9
|
45.5
|
1.0
|
HG11
|
B:VAL289
|
4.9
|
41.6
|
1.0
|
C3
|
B:M3U401
|
5.0
|
53.7
|
1.0
|
|
Reference:
H.Ma,
J.B.Murray,
H.Luo,
X.Cheng,
Q.Chen,
C.Song,
C.Duan,
P.Tan,
L.Zhang,
J.Liu,
B.A.Morgan,
J.Li,
J.Wan,
L.M.Baker,
W.Finnie,
L.Guetzoyan,
R.Harris,
N.Hendrickson,
N.Matassova,
H.Simmonite,
J.Smith,
R.E.Hubbard,
G.Liu.
Pac-Fragmentdel - Photoactivated Covalent Capture of Dna-Encoded Fragments For Hit Discovery. Rsc Med Chem V. 13 1341 2022.
ISSN: ESSN 2632-8682
PubMed: 36426238
DOI: 10.1039/D2MD00197G
Page generated: Fri Aug 2 16:30:20 2024
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