Bromine in PDB 5dht: 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: 5dht
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)
|
66.32 /
2.59
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.781,
119.072,
67.347,
90.00,
100.03,
90.00
|
R / Rfree (%)
|
22.9 /
27.1
|
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 5dht). 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: 5dht:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 5dht
Go back to
Bromine Binding Sites List in 5dht
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:Br303
b:38.9
occ:0.50
|
BR
|
A:5A9303
|
0.0
|
38.9
|
0.5
|
CBD
|
A:5A9303
|
1.9
|
41.5
|
1.0
|
CBE
|
A:5A9303
|
2.8
|
41.5
|
1.0
|
CBC
|
A:5A9303
|
2.8
|
42.4
|
1.0
|
C6
|
A:5A9303
|
3.7
|
39.8
|
1.0
|
NH1
|
C:ARG148
|
3.8
|
69.2
|
1.0
|
C5
|
A:5A9303
|
3.8
|
44.3
|
1.0
|
CD1
|
C:ILE187
|
3.9
|
44.0
|
0.5
|
N1
|
A:5A9303
|
3.9
|
39.7
|
1.0
|
C4
|
A:5A9303
|
4.0
|
46.6
|
1.0
|
C2
|
A:5A9303
|
4.1
|
42.0
|
1.0
|
N3
|
A:5A9303
|
4.1
|
45.0
|
1.0
|
CAV
|
A:5A9303
|
4.1
|
44.0
|
1.0
|
CAX
|
A:5A9303
|
4.1
|
43.0
|
1.0
|
N6
|
A:5A9303
|
4.2
|
37.6
|
1.0
|
N7
|
A:5A9303
|
4.4
|
46.8
|
1.0
|
CG
|
C:ARG148
|
4.4
|
60.0
|
1.0
|
CD
|
C:ARG148
|
4.5
|
62.8
|
1.0
|
CB
|
C:PRO132
|
4.5
|
72.5
|
1.0
|
CB
|
C:ILE187
|
4.6
|
39.3
|
0.9
|
N9
|
A:5A9303
|
4.6
|
52.2
|
1.0
|
CAW
|
A:5A9303
|
4.7
|
43.9
|
1.0
|
CG1
|
C:ILE187
|
4.7
|
41.9
|
0.8
|
C8
|
A:5A9303
|
4.8
|
49.6
|
1.0
|
CA
|
C:GLY149
|
4.9
|
50.9
|
1.0
|
CZ
|
C:ARG148
|
4.9
|
69.1
|
1.0
|
CG2
|
C:ILE187
|
4.9
|
39.7
|
0.8
|
|
Bromine binding site 2 out
of 4 in 5dht
Go back to
Bromine Binding Sites List in 5dht
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:69.8
occ:0.80
|
BR
|
B:5A9302
|
0.0
|
69.8
|
0.8
|
CBD
|
B:5A9302
|
1.8
|
62.4
|
1.0
|
CBC
|
B:5A9302
|
2.7
|
61.5
|
1.0
|
CBE
|
B:5A9302
|
2.7
|
61.6
|
1.0
|
N1
|
B:5A9302
|
3.5
|
44.8
|
1.0
|
NE
|
D:ARG148
|
3.5
|
52.4
|
1.0
|
C6
|
B:5A9302
|
3.5
|
46.4
|
1.0
|
C2
|
B:5A9302
|
3.7
|
44.5
|
1.0
|
C5
|
B:5A9302
|
3.7
|
47.1
|
1.0
|
N3
|
B:5A9302
|
3.9
|
45.8
|
1.0
|
C4
|
B:5A9302
|
3.9
|
46.8
|
1.0
|
CAV
|
B:5A9302
|
4.0
|
61.3
|
1.0
|
CG
|
D:ARG148
|
4.0
|
53.2
|
1.0
|
CAX
|
B:5A9302
|
4.0
|
61.6
|
1.0
|
N6
|
B:5A9302
|
4.0
|
47.7
|
1.0
|
NH2
|
D:ARG148
|
4.1
|
55.5
|
1.0
|
CZ
|
D:ARG148
|
4.2
|
54.6
|
1.0
|
CD
|
D:ARG148
|
4.2
|
52.2
|
1.0
|
N7
|
B:5A9302
|
4.4
|
49.1
|
1.0
|
CA
|
D:GLY149
|
4.4
|
63.3
|
1.0
|
CB
|
D:PRO132
|
4.5
|
63.8
|
1.0
|
CAW
|
B:5A9302
|
4.5
|
61.5
|
1.0
|
N
|
D:GLY149
|
4.6
|
63.3
|
1.0
|
N9
|
B:5A9302
|
4.6
|
50.7
|
1.0
|
O
|
D:GLY149
|
4.7
|
69.3
|
1.0
|
CD1
|
D:ILE187
|
4.8
|
51.4
|
1.0
|
C
|
D:GLY149
|
4.9
|
65.8
|
1.0
|
C8
|
B:5A9302
|
4.9
|
50.7
|
1.0
|
C
|
D:ARG148
|
5.0
|
57.1
|
1.0
|
CB
|
D:ILE187
|
5.0
|
46.1
|
1.0
|
CG
|
D:PRO132
|
5.0
|
66.6
|
1.0
|
|
Bromine binding site 3 out
of 4 in 5dht
Go back to
Bromine Binding Sites List in 5dht
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:47.0
occ:0.50
|
BR
|
C:5A9301
|
0.0
|
47.0
|
0.5
|
CBD
|
C:5A9301
|
1.8
|
40.2
|
1.0
|
CBC
|
C:5A9301
|
2.7
|
41.4
|
1.0
|
CBE
|
C:5A9301
|
2.8
|
40.8
|
1.0
|
NE
|
A:ARG148
|
3.6
|
58.5
|
1.0
|
C5
|
C:5A9301
|
3.7
|
39.5
|
1.0
|
C6
|
C:5A9301
|
3.7
|
38.8
|
1.0
|
C4
|
C:5A9301
|
3.8
|
41.3
|
1.0
|
N1
|
C:5A9301
|
3.9
|
39.0
|
1.0
|
N3
|
C:5A9301
|
4.0
|
39.7
|
1.0
|
C2
|
C:5A9301
|
4.0
|
39.7
|
1.0
|
CAV
|
C:5A9301
|
4.0
|
44.9
|
1.0
|
CAX
|
C:5A9301
|
4.1
|
41.3
|
1.0
|
CG
|
A:ARG148
|
4.1
|
51.4
|
1.0
|
N7
|
C:5A9301
|
4.2
|
40.8
|
1.0
|
CD
|
A:ARG148
|
4.3
|
55.2
|
1.0
|
N6
|
C:5A9301
|
4.3
|
41.4
|
1.0
|
NH2
|
A:ARG148
|
4.3
|
65.5
|
1.0
|
CZ
|
A:ARG148
|
4.3
|
65.0
|
1.0
|
CB
|
A:PRO132
|
4.3
|
57.5
|
1.0
|
N9
|
C:5A9301
|
4.3
|
44.7
|
1.0
|
CA
|
A:GLY149
|
4.5
|
43.8
|
1.0
|
C8
|
C:5A9301
|
4.5
|
43.1
|
1.0
|
CAW
|
C:5A9301
|
4.6
|
42.7
|
1.0
|
CD1
|
A:ILE187
|
4.7
|
46.0
|
0.5
|
N
|
A:GLY149
|
4.7
|
43.0
|
1.0
|
O
|
A:GLY149
|
4.8
|
49.8
|
1.0
|
C
|
A:GLY149
|
5.0
|
46.9
|
1.0
|
|
Bromine binding site 4 out
of 4 in 5dht
Go back to
Bromine Binding Sites List in 5dht
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:Br302
b:95.0
occ:0.60
|
BR
|
D:5A9302
|
0.0
|
95.0
|
0.6
|
CBD
|
D:5A9302
|
1.7
|
0.4
|
1.0
|
CBC
|
D:5A9302
|
2.6
|
1.0
|
1.0
|
CBE
|
D:5A9302
|
2.8
|
0.2
|
1.0
|
N7
|
D:5A9302
|
3.5
|
65.4
|
1.0
|
C5
|
D:5A9302
|
3.6
|
65.0
|
1.0
|
C8
|
D:5A9302
|
3.7
|
66.9
|
1.0
|
C4
|
D:5A9302
|
3.9
|
65.0
|
1.0
|
CAV
|
D:5A9302
|
3.9
|
0.7
|
1.0
|
N9
|
D:5A9302
|
4.0
|
66.3
|
1.0
|
CB
|
B:PRO132
|
4.0
|
75.8
|
1.0
|
CAX
|
D:5A9302
|
4.0
|
0.1
|
1.0
|
C6
|
D:5A9302
|
4.1
|
65.7
|
1.0
|
NH2
|
B:ARG148
|
4.2
|
93.9
|
1.0
|
CG
|
B:PRO132
|
4.3
|
80.2
|
1.0
|
CA
|
B:PRO132
|
4.3
|
74.4
|
1.0
|
SAH
|
D:5A9302
|
4.3
|
67.8
|
1.0
|
N6
|
D:5A9302
|
4.3
|
65.2
|
1.0
|
CZ
|
B:ARG148
|
4.4
|
91.3
|
1.0
|
CAW
|
D:5A9302
|
4.5
|
0.9
|
1.0
|
NAK
|
D:5A9302
|
4.5
|
98.8
|
1.0
|
NH1
|
B:ARG148
|
4.5
|
91.0
|
1.0
|
OAS
|
D:5A9302
|
4.6
|
68.9
|
1.0
|
N3
|
D:5A9302
|
4.6
|
64.0
|
1.0
|
N1
|
D:5A9302
|
4.8
|
65.3
|
1.0
|
O
|
B:GLY149
|
4.8
|
67.2
|
1.0
|
CAR
|
D:5A9302
|
4.8
|
68.2
|
1.0
|
CAM
|
D:5A9302
|
5.0
|
0.1
|
1.0
|
C2
|
D:5A9302
|
5.0
|
64.3
|
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 23:25:26 2024
|