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Chlorine in PDB 6buv: Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate

Enzymatic activity of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate:
2.7.7.18;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate, PDB code: 6buv was solved by I.A.Rodionova, R.W.Reed, L.Sorci, A.L.Osterman, K.V.Korotkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.10 / 1.86
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 163.730, 163.730, 153.650, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 19.2

Other elements in 6buv:

The structure of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate (pdb code 6buv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate, PDB code: 6buv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6buv

Go back to Chlorine Binding Sites List in 6buv
Chlorine binding site 1 out of 5 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:33.9
occ:1.00
 HH21 A:ARG196 2.3 79.4 1.0
HE A:ARG196 3.1 59.4 1.0
NH2 A:ARG196 3.1 66.2 1.0
HE1 A:TYR192 3.3 42.5 1.0
HH22 A:ARG196 3.6 79.4 1.0
NE A:ARG196 3.7 49.5 1.0
CZ A:ARG196 3.8 70.3 1.0
HE3 A:LYS195 3.9 39.8 1.0
HD1 A:TYR192 3.9 33.6 1.0
CE1 A:TYR192 4.0 35.4 1.0
O A:HOH448 4.2 43.0 1.0
CD1 A:TYR192 4.3 28.0 1.0
CE A:LYS195 4.8 33.2 1.0
HZ1 A:LYS195 4.8 35.6 1.0
HD13 A:LEU59 4.9 39.8 1.0
CD A:ARG196 5.0 52.7 1.0
HG2 A:ARG196 5.0 58.2 1.0

Chlorine binding site 2 out of 5 in 6buv

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Chlorine binding site 2 out of 5 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:41.9
occ:1.00
 HG A:SER100 2.3 46.9 1.0
H A:ASP99 2.6 35.9 1.0
HA A:HIS97 3.0 38.1 1.0
OG A:SER100 3.1 39.1 1.0
HB3 A:HIS97 3.1 37.0 1.0
HB2 A:ASP99 3.1 46.2 1.0
O A:HOH467 3.3 56.9 1.0
N A:ASP99 3.3 29.9 1.0
C A:HIS97 3.3 30.8 1.0
H A:SER100 3.4 36.1 1.0
CA A:HIS97 3.5 31.8 1.0
HD3 A:ARG4 3.5 79.6 1.0
N A:SER100 3.6 30.1 1.0
O A:HIS97 3.6 31.1 1.0
HD2 A:PRO98 3.6 41.6 1.0
N A:PRO98 3.7 29.8 1.0
CB A:HIS97 3.8 30.9 1.0
C A:ASP99 3.8 40.2 1.0
CA A:ASP99 3.9 35.0 1.0
CB A:ASP99 3.9 38.5 1.0
CB A:SER100 4.1 36.5 1.0
HB2 A:SER100 4.1 43.8 1.0
HH11 A:ARG4 4.2 84.7 1.0
CD A:PRO98 4.2 34.7 1.0
HD1 A:HIS97 4.3 50.6 1.0
HB2 A:HIS97 4.4 37.0 1.0
C A:PRO98 4.4 35.0 1.0
CA A:SER100 4.4 33.5 1.0
CD A:ARG4 4.4 66.4 1.0
HB3 A:ASP99 4.4 46.2 1.0
HD2 A:ARG4 4.5 79.6 1.0
CA A:PRO98 4.6 34.9 1.0
O A:ASP99 4.6 37.6 1.0
HA A:SER100 4.6 40.2 1.0
HG2 A:PRO98 4.6 47.4 1.0
NH1 A:ARG4 4.8 70.6 1.0
HA A:ASP99 4.8 42.1 1.0
CG A:HIS97 4.8 31.9 1.0
HB3 A:ARG4 4.8 59.5 1.0
N A:HIS97 4.9 29.9 1.0
ND1 A:HIS97 4.9 42.2 1.0
HD3 A:PRO98 4.9 41.6 1.0
HB3 A:SER100 4.9 43.8 1.0
CG A:PRO98 5.0 39.5 1.0

Chlorine binding site 3 out of 5 in 6buv

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Chlorine binding site 3 out of 5 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:56.7
occ:1.00
 H A:GLY119 2.1 46.2 1.0
N A:GLY119 3.0 38.5 1.0
O A:HOH483 3.0 54.3 1.0
HZ3 A:LYS87 3.0 99.5 1.0
HD2 A:TYR85 3.0 34.0 1.0
HB3 A:GLN118 3.2 35.2 1.0
HE2 A:TYR85 3.3 40.7 1.0
HA A:GLN118 3.3 41.9 1.0
HD3 A:LYS87 3.3 69.3 1.0
HE2 A:LYS87 3.4 83.9 1.0
HA3 A:GLY119 3.5 49.6 1.0
O A:HOH418 3.6 30.6 1.0
CD2 A:TYR85 3.7 28.4 1.0
NZ A:LYS87 3.7 83.0 1.0
CE2 A:TYR85 3.8 33.9 1.0
CA A:GLY119 3.8 41.4 1.0
CA A:GLN118 3.8 34.9 1.0
CE A:LYS87 3.8 69.9 1.0
C A:GLN118 3.9 43.2 1.0
CB A:GLN118 3.9 29.4 1.0
HZ1 A:LYS87 4.0 99.5 1.0
CD A:LYS87 4.0 57.8 1.0
HG2 A:GLN118 4.3 34.5 1.0
HZ2 A:LYS87 4.4 99.5 1.0
HA2 A:GLY119 4.5 49.6 1.0
OE1 A:GLU122 4.5 88.1 1.0
HG2 A:LYS87 4.6 43.0 1.0
HB2 A:GLN118 4.7 35.2 1.0
O A:GLY119 4.7 41.3 1.0
CG A:GLN118 4.7 28.8 1.0
HD2 A:LYS87 4.7 69.3 1.0
C A:GLY119 4.7 42.0 1.0
HE3 A:LYS87 4.8 83.9 1.0
HB3 A:TYR85 4.8 38.0 1.0
CG A:TYR85 4.9 33.5 1.0
HB3 A:LYS87 4.9 35.1 1.0
OE1 A:GLN118 4.9 30.1 1.0
CG A:LYS87 4.9 35.8 1.0

Chlorine binding site 4 out of 5 in 6buv

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Chlorine binding site 4 out of 5 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:44.7
occ:1.00
 HH21 B:ARG196 2.6 93.1 1.0
NH2 B:ARG196 3.1 77.6 1.0
HE B:ARG196 3.1 77.3 1.0
HE3 B:LYS195 3.5 63.6 1.0
NE B:ARG196 3.6 64.4 1.0
HE2 B:TYR192 3.6 47.2 1.0
HH22 B:ARG196 3.6 93.1 1.0
CZ B:ARG196 3.6 85.0 1.0
HD2 B:TYR192 4.0 38.8 1.0
O B:HOH455 4.1 54.6 1.0
CE2 B:TYR192 4.3 39.4 1.0
CE B:LYS195 4.5 53.0 1.0
CD2 B:TYR192 4.5 32.3 1.0
NH1 B:ARG196 4.7 93.6 1.0
HG3 B:LYS195 4.7 52.9 1.0
CD B:ARG196 4.8 53.2 1.0
HZ1 B:LYS195 4.8 44.0 1.0
HG2 B:ARG196 4.8 57.2 1.0
HE2 B:LYS195 4.8 63.6 1.0
HD3 B:ARG196 4.9 63.9 1.0
HZ2 B:LYS195 5.0 44.0 1.0

Chlorine binding site 5 out of 5 in 6buv

Go back to Chlorine Binding Sites List in 6buv
Chlorine binding site 5 out of 5 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:44.8
occ:1.00
 HE2 B:HIS17 2.2 34.9 1.0
HH12 B:ARG134 2.4 83.5 1.0
H B:SER168 2.4 36.0 1.0
HH22 B:ARG134 2.7 54.6 1.0
HA B:SER167 2.8 38.7 1.0
O B:HOH482 3.0 60.0 1.0
NE2 B:HIS17 3.1 29.1 1.0
HE2 B:HIS20 3.2 45.0 1.0
NH1 B:ARG134 3.2 69.6 1.0
N B:SER168 3.2 29.9 1.0
NH2 B:ARG134 3.4 45.5 1.0
NE2 B:HIS20 3.6 37.5 1.0
CA B:SER167 3.6 32.2 1.0
HB2 B:SER168 3.7 37.1 1.0
HB2 B:SER167 3.7 43.5 1.0
OG B:SER168 3.8 31.4 1.0
CZ B:ARG134 3.8 72.9 1.0
HE1 B:HIS17 3.8 41.5 1.0
CE1 B:HIS17 3.8 34.6 1.0
O B:HOH473 3.8 27.3 1.0
HH11 B:ARG134 3.9 83.5 1.0
O B:HOH531 3.9 58.6 1.0
C B:SER167 3.9 30.3 1.0
HE1 B:HIS20 4.0 44.9 1.0
CE1 B:HIS20 4.1 37.4 1.0
CB B:SER168 4.1 30.9 1.0
HH21 B:ARG134 4.1 54.6 1.0
CB B:SER167 4.2 36.3 1.0
CD2 B:HIS17 4.2 28.6 1.0
O B:ILE166 4.2 30.9 1.0
CA B:SER168 4.3 27.6 1.0
HD22 B:LEU164 4.3 42.0 1.0
HG B:SER168 4.3 37.7 1.0
HD2 B:HIS17 4.4 34.3 1.0
HB3 B:SER167 4.5 43.5 1.0
CD2 B:HIS20 4.5 36.5 1.0
N B:SER167 4.8 31.5 1.0
HA B:SER168 4.8 33.1 1.0
H B:THR169 4.8 38.8 1.0
HD2 B:HIS20 4.8 43.8 1.0
C B:ILE166 4.9 35.3 1.0

Reference:

A.L.Osterman, I.Rodionova, X.Li, E.Sergienko, C.T.Ma, A.Catanzaro, M.E.Pettigrove, R.W.Reed, R.Gupta, K.H.Rohde, K.V.Korotkov, L.Sorci. Novel Antimycobacterial Compounds Suppress Nad Biogenesis By Targeting A Unique Pocket of Namn Adenylyltransferase. Acs Chem.Biol. V. 14 949 2019.
ISSN: ESSN 1554-8937
PubMed: 30969758
DOI: 10.1021/ACSCHEMBIO.9B00124
Page generated: Fri Jul 26 23:06:25 2024

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