Chlorine in PDB 7ok1: Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3

Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3

All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3:
2.3.1.129;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3, PDB code: 7ok1 was solved by M.D.Ryan, A.L.Parkes, M.Southey, O.A.Andersen, M.Zahn, J.Barker, B.L.M.Dejonge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.67 / 1.92
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 166.046, 166.046, 98.54, 90, 90, 90
R / Rfree (%) 19.1 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 (pdb code 7ok1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3, PDB code: 7ok1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 7ok1

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Chlorine binding site 1 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:31.9
occ:1.00
 CL1 A:VFN301 0.0 31.9 1.0
C26 A:VFN301 1.7 28.4 1.0
C21 A:VFN301 2.7 29.1 1.0
C25 A:VFN301 2.7 26.5 1.0
S20 A:VFN301 3.1 30.2 1.0
CA A:GLY151 3.6 27.3 1.0
CB B:ALA136 3.7 23.6 1.0
CD1 A:TYR152 3.9 28.1 1.0
C22 A:VFN301 4.0 26.9 1.0
C24 A:VFN301 4.0 28.3 1.0
C A:GLY151 4.2 31.2 1.0
CE1 A:TYR152 4.3 27.8 1.0
CD2 B:LEU154 4.3 29.4 1.0
CB B:LEU154 4.4 25.9 1.0
O A:GLY151 4.5 30.4 1.0
N A:GLY151 4.5 26.6 1.0
C23 A:VFN301 4.5 27.0 1.0
CG B:LEU154 4.7 28.2 1.0
CB A:MET169 4.8 32.4 1.0
SD A:MET169 4.8 37.6 1.0
O B:ALA136 4.8 31.3 1.0
C19 A:VFN301 4.8 31.2 1.0
CD1 B:LEU154 4.9 24.8 1.0
N A:TYR152 4.9 28.7 1.0
CA B:ALA136 5.0 23.8 1.0
C B:ALA136 5.0 29.3 1.0

Chlorine binding site 2 out of 9 in 7ok1

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Chlorine binding site 2 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:35.0
occ:1.00
 CL1 A:VFN302 0.0 35.0 1.0
C26 A:VFN302 1.7 33.0 1.0
C21 A:VFN302 2.7 31.1 1.0
C25 A:VFN302 2.7 30.4 1.0
S20 A:VFN302 3.1 30.0 1.0
CA C:GLY151 3.7 30.5 1.0
CB A:ALA136 3.7 28.1 1.0
CD1 C:TYR152 4.0 30.6 1.0
C24 A:VFN302 4.0 29.1 1.0
C22 A:VFN302 4.0 28.3 1.0
C C:GLY151 4.1 32.4 1.0
CE1 C:TYR152 4.3 29.2 1.0
CD2 A:LEU154 4.3 25.8 1.0
O C:GLY151 4.3 31.1 1.0
N C:GLY151 4.5 31.1 1.0
C23 A:VFN302 4.5 28.3 1.0
CB A:LEU154 4.6 25.0 1.0
SD C:MET169 4.6 42.0 1.0
CB C:MET169 4.6 36.6 1.0
O A:ALA136 4.7 28.2 1.0
CG A:LEU154 4.8 27.5 1.0
C19 A:VFN302 4.8 31.4 1.0
CD1 A:LEU154 4.8 26.9 1.0
C A:ALA136 4.9 29.4 1.0
CA A:ALA136 5.0 27.5 1.0
N C:TYR152 5.0 27.8 1.0

Chlorine binding site 3 out of 9 in 7ok1

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Chlorine binding site 3 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:34.6
occ:1.00
 O A:HOH415 2.9 33.8 1.0
CG B:PRO69 3.3 65.0 1.0
N A:ALA115 3.3 28.2 1.0
CG A:ARG89 3.5 29.4 1.0
CB A:ALA115 3.6 27.4 1.0
CB A:ARG89 3.6 24.6 1.0
NE A:ARG89 3.7 39.4 1.0
CB A:MET114 3.7 28.6 1.0
OD1 A:ASN133 3.9 27.0 1.0
CA A:MET114 4.0 26.6 1.0
OE2 A:GLU90 4.0 71.7 1.0
CA A:ALA115 4.0 27.8 1.0
CE A:MET114 4.1 33.2 1.0
C A:MET114 4.1 29.9 1.0
CD A:ARG89 4.1 34.8 1.0
CD B:PRO69 4.2 60.8 1.0
ND2 A:ASN133 4.2 31.0 1.0
CG A:MET114 4.2 31.8 1.0
CE1 B:HIS95 4.3 41.3 1.0
CB B:PRO69 4.4 61.3 1.0
CG A:ASN133 4.4 39.6 1.0
CZ A:ARG89 4.5 55.1 1.0
CD A:GLU90 4.5 63.1 1.0
NE2 B:HIS95 4.6 41.9 1.0
OE1 A:GLU90 4.6 48.4 1.0
NH2 A:ARG89 4.7 46.8 1.0
SD A:MET114 5.0 37.0 1.0

Chlorine binding site 4 out of 9 in 7ok1

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Chlorine binding site 4 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:48.0
occ:1.00
 O A:HOH452 3.0 30.6 1.0
N A:MET169 3.2 29.6 1.0
O B:HOH518 3.3 37.8 1.0
CA A:GLY168 3.6 27.5 1.0
C A:GLY168 3.9 32.0 1.0
CG A:MET169 4.2 34.9 1.0
CB A:MET169 4.2 32.4 1.0
CE2 A:PHE184 4.3 37.1 1.0
CA A:MET169 4.3 30.0 1.0
CD2 B:HIS156 4.5 40.3 1.0
OG A:SER150 4.6 31.2 1.0
CZ A:PHE166 4.7 32.6 1.0
CD2 A:PHE184 4.7 34.2 1.0
CB A:SER150 4.9 27.3 1.0
CE2 A:PHE166 4.9 35.7 1.0
SD A:MET169 5.0 37.6 1.0

Chlorine binding site 5 out of 9 in 7ok1

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Chlorine binding site 5 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:52.9
occ:1.00
 NH1 A:ARG199 3.3 41.2 1.0
CD A:ARG199 3.6 38.1 1.0
CG A:GLU196 3.8 46.5 1.0
CA A:GLU196 3.9 37.2 1.0
CZ A:ARG199 4.2 60.1 1.0
N A:GLU196 4.3 35.6 1.0
NE A:ARG199 4.3 44.5 1.0
CB A:GLU196 4.4 38.9 1.0
CG A:ARG199 4.4 40.5 1.0
C A:PHE195 4.6 38.1 1.0
O A:PHE195 4.7 38.6 1.0
CB A:ARG199 4.7 37.4 1.0
CD A:GLU196 4.9 61.8 1.0
O A:HOH471 4.9 43.6 1.0
OE1 A:GLU196 5.0 57.5 1.0

Chlorine binding site 6 out of 9 in 7ok1

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Chlorine binding site 6 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:35.1
occ:1.00
 O A:HOH472 3.2 27.8 1.0
O A:HOH420 3.2 38.1 1.0
NZ A:LYS54 3.3 36.8 1.0
CA A:GLY35 3.7 31.0 1.0
CA A:GLY53 3.9 28.1 1.0
CG A:LYS54 3.9 29.9 1.0
C A:GLY53 4.0 31.7 1.0
O A:HOH409 4.1 44.5 1.0
N A:LYS54 4.1 28.8 1.0
CE A:LYS51 4.2 30.2 1.0
CE A:LYS54 4.3 37.4 1.0
N A:GLY35 4.4 31.2 1.0
NZ A:LYS51 4.5 41.8 1.0
O A:ILE52 4.5 34.0 1.0
CD A:LYS54 4.6 29.9 1.0
C A:GLY35 4.7 32.2 1.0
O A:GLY53 4.7 29.1 1.0
N A:GLU36 4.7 30.8 1.0
CB A:LYS54 4.9 28.9 1.0
CA A:LYS54 4.9 27.7 1.0
N A:GLY53 5.0 29.3 1.0
OD1 A:ASP84 5.0 34.4 1.0

Chlorine binding site 7 out of 9 in 7ok1

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Chlorine binding site 7 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:33.5
occ:1.00
 O A:HOH450 3.2 30.8 1.0
CZ A:ARG15 3.8 53.6 1.0
NE A:ARG15 3.9 44.2 1.0
NH2 A:ARG15 3.9 40.6 1.0
CD A:ARG15 3.9 44.2 1.0
NH1 A:ARG15 4.4 37.5 1.0
OE2 A:GLU31 4.5 49.6 1.0

Chlorine binding site 8 out of 9 in 7ok1

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Chlorine binding site 8 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:35.6
occ:1.00
 CL1 B:VFN301 0.0 35.6 1.0
C26 B:VFN301 1.7 34.5 1.0
C25 B:VFN301 2.7 33.7 1.0
C21 B:VFN301 2.7 32.3 1.0
S20 B:VFN301 3.1 29.3 1.0
CA B:GLY151 3.6 30.2 1.0
CB C:ALA136 3.7 27.2 1.0
CD1 B:TYR152 3.9 31.7 1.0
C24 B:VFN301 4.0 31.9 1.0
C22 B:VFN301 4.0 31.9 1.0
C B:GLY151 4.1 33.9 1.0
CD2 C:LEU154 4.2 32.6 1.0
CE1 B:TYR152 4.3 33.0 1.0
N B:GLY151 4.4 30.5 1.0
O B:GLY151 4.5 33.4 1.0
CB C:LEU154 4.5 28.7 1.0
C23 B:VFN301 4.5 31.5 1.0
SD B:MET169 4.7 39.2 1.0
CG C:LEU154 4.7 32.2 1.0
CB B:MET169 4.8 32.0 1.0
O C:ALA136 4.8 32.1 1.0
CD1 C:LEU154 4.8 31.1 1.0
N B:TYR152 4.8 29.9 1.0
C19 B:VFN301 4.9 30.3 1.0
CA C:ALA136 4.9 26.5 1.0

Chlorine binding site 9 out of 9 in 7ok1

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Chlorine binding site 9 out of 9 in the Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Pseudomonas Aeruginosa Lpxa in Complex with Compound 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:73.4
occ:1.00
 O C:HOH491 3.1 44.2 1.0
CD1 C:ILE130 3.8 32.0 1.0
C11 A:VFN302 4.0 31.8 1.0
CD1 C:ILE148 4.1 28.9 1.0
CZ C:ARG200 4.2 109.2 1.0
NE C:ARG200 4.3 97.5 1.0
NH2 C:ARG200 4.3 81.0 1.0
CD2 A:LEU71 4.3 56.2 1.0
O C:HOH447 4.5 42.7 1.0
NH1 C:ARG200 4.5 104.2 1.0
CD C:ARG200 4.6 86.7 1.0
C10 A:VFN302 4.7 27.8 1.0
C15 A:VFN302 4.8 38.7 1.0
C12 A:VFN302 4.9 34.6 1.0

Reference:

M.D.Ryan, A.L.Parkes, D.Corbett, A.P.Dickie, M.Southey, O.A.Andersen, D.B.Stein, O.R.Barbeau, A.Sanzone, P.Thommes, J.Barker, R.Cain, C.Compper, M.Dejob, A.Dorali, D.Etheridge, S.Evans, A.Faulkner, E.Gadouleau, T.Gorman, D.Haase, M.Holbrow-Wilshaw, T.Krulle, X.Li, C.Lumley, B.Mertins, S.Napier, R.Odedra, K.Papadopoulos, V.Roumpelakis, K.Spear, E.Trimby, J.Williams, M.Zahn, A.D.Keefe, Y.Zhang, H.T.Soutter, P.A.Centrella, M.A.Clark, J.W.Cuozzo, C.E.Dumelin, B.Deng, A.Hunt, E.A.Sigel, D.M.Troast, B.L.M.Dejonge. Discovery of Novel Udp- N -Acetylglucosamine Acyltransferase (Lpxa) Inhibitors with Activity Against Pseudomonas Aeruginosa . J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34569791
DOI: 10.1021/ACS.JMEDCHEM.1C00888
Page generated: Tue Jul 30 01:34:13 2024

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