Bromine in PDB 5dhq: Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
Enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
All present enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor:
2.7.1.23;
Protein crystallography data
The structure of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor, PDB code: 5dhq
was solved by
M.Gelin,
J.Paoletti,
L.Assairi,
V.Huteau,
S.Pochet,
G.Labesse,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.29 /
2.29
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.790,
119.180,
67.210,
90.00,
99.91,
90.00
|
R / Rfree (%)
|
26 /
31.1
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
(pdb code 5dhq). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor, PDB code: 5dhq:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 5dhq
Go back to
Bromine Binding Sites List in 5dhq
Bromine binding site 1 out
of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br302
b:70.8
occ:1.00
|
BR
|
A:5AK302
|
0.0
|
70.8
|
1.0
|
CAW
|
A:5AK302
|
1.9
|
30.2
|
1.0
|
CAI
|
A:5AK302
|
2.8
|
26.9
|
1.0
|
CAK
|
A:5AK302
|
2.8
|
29.9
|
1.0
|
NH1
|
C:ARG148
|
3.3
|
56.3
|
1.0
|
C6
|
A:5AK302
|
3.6
|
17.0
|
1.0
|
N1
|
A:5AK302
|
3.6
|
17.3
|
1.0
|
C5
|
A:5AK302
|
3.6
|
20.2
|
1.0
|
CZ
|
C:ARG148
|
3.6
|
53.2
|
1.0
|
C4
|
A:5AK302
|
3.6
|
20.5
|
1.0
|
N3
|
A:5AK302
|
3.7
|
20.1
|
1.0
|
C2
|
A:5AK302
|
3.7
|
20.6
|
1.0
|
NH2
|
C:ARG148
|
3.9
|
49.0
|
1.0
|
CAG
|
A:5AK302
|
4.1
|
39.6
|
1.0
|
CAY
|
A:5AK302
|
4.1
|
30.6
|
1.0
|
N6
|
A:5AK302
|
4.2
|
20.6
|
1.0
|
N7
|
A:5AK302
|
4.3
|
25.3
|
1.0
|
NE
|
C:ARG148
|
4.3
|
57.5
|
1.0
|
CG2
|
C:ILE187
|
4.3
|
61.2
|
1.0
|
N9
|
A:5AK302
|
4.3
|
24.1
|
1.0
|
CG
|
C:ARG148
|
4.4
|
56.4
|
1.0
|
CA
|
C:GLY149
|
4.6
|
52.6
|
1.0
|
C8
|
A:5AK302
|
4.7
|
22.3
|
1.0
|
CAJ
|
A:5AK302
|
4.7
|
41.0
|
1.0
|
CB
|
C:PRO132
|
4.7
|
41.9
|
1.0
|
CD
|
C:ARG148
|
4.7
|
51.7
|
1.0
|
N
|
C:GLY149
|
4.8
|
54.0
|
1.0
|
CD1
|
C:ILE187
|
4.8
|
72.1
|
1.0
|
CB
|
C:ILE187
|
5.0
|
62.3
|
1.0
|
|
Bromine binding site 2 out
of 4 in 5dhq
Go back to
Bromine Binding Sites List in 5dhq
Bromine binding site 2 out
of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br302
b:61.9
occ:0.80
|
BR
|
B:5AK302
|
0.0
|
61.9
|
0.8
|
CAW
|
B:5AK302
|
1.7
|
72.3
|
1.0
|
CAK
|
B:5AK302
|
2.6
|
65.1
|
1.0
|
CAI
|
B:5AK302
|
2.7
|
73.1
|
1.0
|
C6
|
B:5AK302
|
3.6
|
44.9
|
1.0
|
N1
|
B:5AK302
|
3.6
|
47.3
|
1.0
|
C5
|
B:5AK302
|
3.7
|
53.0
|
1.0
|
NE
|
D:ARG148
|
3.7
|
50.2
|
1.0
|
NH2
|
D:ARG148
|
3.7
|
58.6
|
1.0
|
C2
|
B:5AK302
|
3.7
|
42.7
|
1.0
|
C4
|
B:5AK302
|
3.8
|
53.1
|
1.0
|
N3
|
B:5AK302
|
3.8
|
41.8
|
1.0
|
CZ
|
D:ARG148
|
3.9
|
56.5
|
1.0
|
CAY
|
B:5AK302
|
3.9
|
66.9
|
1.0
|
CAG
|
B:5AK302
|
3.9
|
74.3
|
1.0
|
N6
|
B:5AK302
|
4.1
|
45.5
|
1.0
|
CG
|
D:ARG148
|
4.2
|
45.2
|
1.0
|
N7
|
B:5AK302
|
4.3
|
55.7
|
1.0
|
CA
|
D:GLY149
|
4.4
|
69.3
|
1.0
|
N9
|
B:5AK302
|
4.4
|
54.0
|
1.0
|
CAJ
|
B:5AK302
|
4.4
|
73.6
|
1.0
|
CB
|
D:PRO132
|
4.5
|
62.9
|
1.0
|
CD
|
D:ARG148
|
4.5
|
52.7
|
1.0
|
N
|
D:GLY149
|
4.6
|
71.1
|
1.0
|
O
|
D:GLY149
|
4.6
|
75.9
|
1.0
|
C8
|
B:5AK302
|
4.7
|
56.1
|
1.0
|
NH1
|
D:ARG148
|
4.8
|
71.7
|
1.0
|
C
|
D:GLY149
|
4.8
|
68.7
|
1.0
|
CG
|
D:PRO132
|
5.0
|
49.9
|
1.0
|
|
Bromine binding site 3 out
of 4 in 5dhq
Go back to
Bromine Binding Sites List in 5dhq
Bromine binding site 3 out
of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br301
b:0.2
occ:1.00
|
BR
|
C:5AK301
|
0.0
|
0.2
|
1.0
|
CAW
|
C:5AK301
|
1.7
|
38.4
|
1.0
|
CAI
|
C:5AK301
|
2.7
|
31.0
|
1.0
|
CAK
|
C:5AK301
|
2.7
|
30.5
|
1.0
|
NE
|
A:ARG148
|
3.5
|
51.1
|
1.0
|
C6
|
C:5AK301
|
3.6
|
31.4
|
1.0
|
C5
|
C:5AK301
|
3.7
|
29.8
|
1.0
|
N1
|
C:5AK301
|
3.7
|
29.7
|
1.0
|
C4
|
C:5AK301
|
3.9
|
32.7
|
1.0
|
CG
|
A:ARG148
|
4.0
|
33.7
|
1.0
|
CAG
|
C:5AK301
|
4.0
|
29.8
|
1.0
|
CAY
|
C:5AK301
|
4.0
|
36.6
|
1.0
|
C2
|
C:5AK301
|
4.0
|
27.7
|
1.0
|
N3
|
C:5AK301
|
4.0
|
27.6
|
1.0
|
N6
|
C:5AK301
|
4.1
|
31.5
|
1.0
|
CZ
|
A:ARG148
|
4.1
|
62.5
|
1.0
|
NH1
|
A:ARG148
|
4.2
|
62.8
|
1.0
|
CD
|
A:ARG148
|
4.2
|
55.2
|
1.0
|
CB
|
A:PRO132
|
4.2
|
39.3
|
1.0
|
N7
|
C:5AK301
|
4.3
|
28.4
|
1.0
|
CA
|
A:GLY149
|
4.4
|
37.6
|
1.0
|
CAJ
|
C:5AK301
|
4.5
|
29.7
|
1.0
|
N
|
A:GLY149
|
4.5
|
29.8
|
1.0
|
N9
|
C:5AK301
|
4.5
|
41.0
|
1.0
|
C8
|
C:5AK301
|
4.8
|
41.5
|
1.0
|
CD1
|
A:ILE187
|
4.8
|
36.2
|
0.5
|
O
|
A:GLY149
|
4.9
|
38.1
|
1.0
|
C
|
A:ARG148
|
4.9
|
36.5
|
1.0
|
CA
|
A:PRO132
|
4.9
|
39.3
|
1.0
|
C
|
A:GLY149
|
4.9
|
41.0
|
1.0
|
CB
|
A:ILE187
|
5.0
|
29.7
|
1.0
|
|
Bromine binding site 4 out
of 4 in 5dhq
Go back to
Bromine Binding Sites List in 5dhq
Bromine binding site 4 out
of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br301
b:0.2
occ:1.00
|
BR
|
D:5AK301
|
0.0
|
0.2
|
1.0
|
CAW
|
D:5AK301
|
1.8
|
81.8
|
1.0
|
CAI
|
D:5AK301
|
2.7
|
73.3
|
1.0
|
CAK
|
D:5AK301
|
2.7
|
81.7
|
1.0
|
C6
|
D:5AK301
|
3.5
|
47.2
|
1.0
|
C5
|
D:5AK301
|
3.5
|
47.7
|
1.0
|
NH2
|
B:ARG148
|
3.6
|
68.7
|
1.0
|
N1
|
D:5AK301
|
3.7
|
49.0
|
1.0
|
C4
|
D:5AK301
|
3.8
|
41.9
|
1.0
|
CZ
|
B:ARG148
|
3.8
|
70.4
|
1.0
|
NE
|
B:ARG148
|
3.9
|
67.1
|
1.0
|
N6
|
D:5AK301
|
3.9
|
40.7
|
1.0
|
N7
|
D:5AK301
|
4.0
|
48.2
|
1.0
|
CAG
|
D:5AK301
|
4.0
|
67.5
|
1.0
|
CAY
|
D:5AK301
|
4.0
|
77.7
|
1.0
|
N3
|
D:5AK301
|
4.1
|
40.5
|
1.0
|
C2
|
D:5AK301
|
4.1
|
50.4
|
1.0
|
O
|
D:HOH419
|
4.3
|
79.8
|
1.0
|
CG2
|
B:ILE187
|
4.3
|
82.8
|
1.0
|
N9
|
D:5AK301
|
4.4
|
50.5
|
1.0
|
C8
|
D:5AK301
|
4.5
|
59.5
|
1.0
|
CAJ
|
D:5AK301
|
4.5
|
71.6
|
1.0
|
CG
|
B:ARG148
|
4.5
|
65.1
|
1.0
|
NH1
|
B:ARG148
|
4.7
|
72.3
|
1.0
|
CD
|
B:ARG148
|
4.8
|
67.6
|
1.0
|
CB
|
B:PRO132
|
4.8
|
68.7
|
1.0
|
CA
|
B:GLY149
|
4.9
|
45.6
|
1.0
|
|
Reference:
J.Paoletti,
L.Assairi,
M.Gelin,
V.Huteau,
M.A.Nahori,
O.Dussurget,
G.Labesse,
S.Pochet.
8-Thioalkyl-Adenosine Derivatives Inhibit Listeria Monocytogenes Nad Kinase Through A Novel Binding Mode. Eur.J.Med.Chem. V. 124 1041 2016.
ISSN: ISSN 0223-5234
PubMed: 27783975
DOI: 10.1016/J.EJMECH.2016.10.033
Page generated: Wed Jul 10 23:24:41 2024
|