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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: Sat Dec 12 02:25:21 2020

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