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Sodium in PDB 8otm: Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide

Enzymatic activity of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide

All present enzymatic activity of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide:
1.3.1.9;

Protein crystallography data

The structure of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide, PDB code: 8otm was solved by M.Chebaiki, L.Maveyraud, R.Tamhaev, C.Lherbet, L.Mourey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.07 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.588, 92.784, 90.751, 90, 119.2, 90
R / Rfree (%) 15.9 / 17.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide (pdb code 8otm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide, PDB code: 8otm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8otm

Go back to Sodium Binding Sites List in 8otm
Sodium binding site 1 out of 5 in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:19.8
occ:0.81
 O A:HOH646 2.2 37.4 1.0
O A:HOH588 2.3 33.7 1.0
O A:HOH655 2.4 31.9 1.0
O A:ASP223 2.4 17.2 1.0
O A:ALA226 2.4 16.9 1.0
O A:GLN224 2.7 22.4 1.0
C A:GLN224 3.3 19.8 1.0
C A:ALA226 3.5 16.6 1.0
C A:ASP223 3.5 16.9 1.0
CA A:GLN224 3.6 18.5 1.0
N A:GLN224 4.0 16.4 1.0
N A:ALA226 4.0 17.0 1.0
N A:GLY229 4.2 17.6 1.0
CA A:ALA226 4.3 16.7 1.0
O A:HOH422 4.3 49.4 1.0
N A:ARG225 4.3 18.1 1.0
CA A:GLY229 4.3 17.3 1.0
N A:PRO227 4.4 16.5 1.0
O A:HOH551 4.4 31.9 1.0
CA A:PRO227 4.4 17.2 1.0
C A:ARG225 4.4 18.1 1.0
C A:PRO227 4.5 18.3 1.0
O A:PRO227 4.5 20.0 1.0
CB A:ALA226 4.6 16.7 1.0
CA A:ASP223 4.8 15.4 1.0
O A:ARG225 4.9 17.8 1.0
O2 A:EDO304 4.9 24.7 0.7
CA A:ARG225 4.9 18.6 1.0
CB A:GLN224 5.0 22.0 1.0
OD1 A:ASP223 5.0 19.1 1.0

Sodium binding site 2 out of 5 in 8otm

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Sodium binding site 2 out of 5 in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:24.9
occ:0.82
 O B:HOH615 2.4 39.0 1.0
O B:HOH464 2.4 43.5 1.0
O B:ASP223 2.4 23.3 1.0
O B:ALA226 2.5 18.2 1.0
O B:GLN224 2.8 25.2 1.0
C B:GLN224 3.4 23.7 1.0
C B:ALA226 3.5 18.5 1.0
C B:ASP223 3.5 22.4 1.0
CA B:GLN224 3.6 23.9 1.0
N B:GLN224 4.0 22.6 1.0
N B:ALA226 4.1 19.4 1.0
N B:GLY229 4.2 20.4 1.0
CA B:GLY229 4.2 19.8 1.0
CA B:ALA226 4.3 19.1 1.0
N B:ARG225 4.4 22.2 1.0
O B:HOH485 4.4 41.6 1.0
O B:HOH533 4.4 39.1 1.0
N B:PRO227 4.4 18.4 1.0
CA B:PRO227 4.4 19.2 1.0
O B:PRO227 4.5 20.3 1.0
C B:PRO227 4.5 19.7 1.0
C B:ARG225 4.5 22.4 1.0
CB B:ALA226 4.8 19.5 1.0
O1 B:EDO303 4.8 34.5 0.8
CA B:ASP223 4.8 21.2 1.0
OD1 B:ASP223 5.0 24.6 1.0
O B:ARG225 5.0 22.5 1.0
CA B:ARG225 5.0 23.3 1.0
CG B:ASP223 5.0 26.7 1.0

Sodium binding site 3 out of 5 in 8otm

Go back to Sodium Binding Sites List in 8otm
Sodium binding site 3 out of 5 in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:21.1
occ:0.78
 O C:HOH662 2.2 36.1 1.0
O C:ASP223 2.4 17.3 1.0
O C:ALA226 2.4 15.5 1.0
O C:HOH628 2.4 34.3 1.0
O C:HOH669 2.5 40.9 1.0
O C:GLN224 2.6 20.7 1.0
C C:GLN224 3.2 19.1 1.0
C C:ALA226 3.5 15.8 1.0
C C:ASP223 3.5 17.1 1.0
CA C:GLN224 3.6 18.6 1.0
N C:GLN224 4.0 17.1 1.0
O C:HOH518 4.0 47.7 1.0
N C:ALA226 4.0 16.6 1.0
N C:GLY229 4.2 17.1 1.0
O C:HOH527 4.2 39.3 1.0
N C:ARG225 4.2 18.4 1.0
O C:HOH523 4.3 35.7 1.0
CA C:GLY229 4.3 16.6 1.0
CA C:ALA226 4.3 15.5 1.0
C C:ARG225 4.4 18.4 1.0
N C:PRO227 4.4 15.5 1.0
CA C:PRO227 4.4 15.6 1.0
O C:HOH584 4.4 52.7 1.0
O C:PRO227 4.4 19.5 1.0
C C:PRO227 4.4 16.8 1.0
CB C:ALA226 4.7 15.1 1.0
CA C:ASP223 4.8 15.3 1.0
CA C:ARG225 4.8 19.6 1.0
OD1 C:ASP223 4.9 17.1 1.0
O C:ARG225 4.9 18.7 1.0

Sodium binding site 4 out of 5 in 8otm

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Sodium binding site 4 out of 5 in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:22.5
occ:0.75
 O D:HOH604 2.2 39.0 1.0
O D:HOH599 2.2 41.4 1.0
O D:ALA226 2.4 18.7 1.0
O D:ASP223 2.5 21.1 1.0
O D:HOH611 2.5 43.9 1.0
O D:GLN224 2.7 24.7 1.0
C D:GLN224 3.3 23.2 1.0
C D:ALA226 3.4 18.9 1.0
C D:ASP223 3.6 21.5 1.0
CA D:GLN224 3.7 23.6 1.0
N D:ALA226 4.0 19.7 1.0
O D:HOH590 4.1 53.3 1.0
N D:GLN224 4.1 22.1 1.0
N D:GLY229 4.2 20.1 1.0
CA D:ALA226 4.2 18.9 1.0
N D:PRO227 4.3 18.3 1.0
CA D:PRO227 4.3 18.2 1.0
N D:ARG225 4.3 21.3 1.0
CA D:GLY229 4.3 20.0 1.0
C D:ARG225 4.3 20.9 1.0
C D:PRO227 4.4 19.1 1.0
O D:PRO227 4.5 20.1 1.0
CB D:ALA226 4.7 19.1 1.0
O D:HOH488 4.7 38.6 1.0
O D:ARG225 4.8 20.5 1.0
CA D:ASP223 4.9 20.6 1.0
CA D:ARG225 4.9 22.1 1.0
N D:ILE228 5.0 19.3 1.0

Sodium binding site 5 out of 5 in 8otm

Go back to Sodium Binding Sites List in 8otm
Sodium binding site 5 out of 5 in the Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Inha From Mycobacterium Tuberculosis in Complex with N- ((1-(3-Hydroxy-4-Phenoxybenzyl)-1H-1,2,3-Triazol-4-Yl)Methyl)-2-Oxo- 2H-Chromene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:33.0
occ:0.43
 O D:HOH430 2.2 44.1 1.0
OD1 D:ASP248 2.7 32.2 1.0
O D:HOH490 2.8 32.1 1.0
O D:LEU246 3.0 19.8 1.0
O D:SER247 3.0 20.3 1.0
NH1 D:ARG185 3.0 26.1 1.0
C D:SER247 3.1 19.7 1.0
O D:GLY141 3.3 22.1 1.0
N D:ASP248 3.5 19.7 1.0
NZ D:LYS8 3.6 34.7 1.0
CE D:LYS8 3.7 33.9 1.0
CG D:ASP248 3.7 31.3 1.0
CA D:ASP248 3.8 20.6 1.0
C D:LEU246 3.8 19.0 1.0
CA D:SER247 3.9 18.5 1.0
N D:SER247 4.2 18.4 1.0
O D:HOH612 4.2 42.1 1.0
O D:HOH470 4.3 30.8 1.0
CZ D:ARG185 4.3 25.4 1.0
CD D:LYS8 4.3 30.2 1.0
CB D:ASP248 4.4 24.1 1.0
C D:GLY141 4.5 20.9 1.0
OD2 D:ASP248 4.7 36.7 1.0
CB D:SER143 4.9 17.5 1.0
CA D:LEU246 4.9 17.9 1.0
NH2 D:ARG185 5.0 27.8 1.0

Reference:

M.Chebaiki, E.Delfourne, R.Tamhaev, S.Danoun, F.Rodriguez, P.Hoffmann, E.Grosjean, F.Goncalves, J.Azema-Despeyroux, A.Pal, J.Kordulakova, N.Preuilh, S.Britton, P.Constant, H.Marrakchi, L.Maveyraud, L.Mourey, C.Lherbet. Discovery of New Diaryl Ether Inhibitors Against Mycobacterium Tuberculosis Targeting the Minor Portal of Inha. Eur.J.Med.Chem. V. 259 15646 2023.
ISSN: ISSN 0223-5234
PubMed: 37482022
DOI: 10.1016/J.EJMECH.2023.115646
Page generated: Wed Oct 9 12:47:35 2024

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