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Fluorine in PDB 7ci5: Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor

Enzymatic activity of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci5 was solved by M.Mima, L.M.Baker, A.Surgenor, A.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.78 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.311, 50.470, 145.857, 76.73, 76.94, 60.85
R / Rfree (%) 21.1 / 28.3

Other elements in 7ci5:

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7ci5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7ci5

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Fluorine binding site 1 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:50.7
occ:1.00
 F13 A:FXX301 0.0 50.7 1.0
C A:FXX301 1.3 50.7 1.0
F14 A:FXX301 2.1 53.4 1.0
F16 A:FXX301 2.2 50.4 1.0
O7 A:FXX301 2.2 49.3 1.0
C2 A:FXX301 2.7 45.3 1.0
C1 A:FXX301 3.1 43.9 1.0
CB A:ALA214 3.4 49.3 1.0
C3 A:FXX301 3.6 44.4 1.0
CA A:GLY192 4.0 53.0 1.0
C6 A:FXX301 4.2 45.3 1.0
CG1 A:ILE197 4.3 68.7 1.0
CD1 A:ILE197 4.4 70.5 1.0
N A:GLY192 4.6 47.6 1.0
C4 A:FXX301 4.6 43.1 1.0
O A:HOH432 4.6 29.8 1.0
CA A:GLY209 4.7 45.6 1.0
C5 A:FXX301 4.8 44.3 1.0
CG2 A:THR190 4.9 35.5 1.0
OD1 A:ASN213 4.9 43.3 1.0
CA A:ALA214 4.9 51.4 1.0

Fluorine binding site 2 out of 12 in 7ci5

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Fluorine binding site 2 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:53.4
occ:1.00
 F14 A:FXX301 0.0 53.4 1.0
C A:FXX301 1.3 50.7 1.0
F16 A:FXX301 2.1 50.4 1.0
F13 A:FXX301 2.1 50.7 1.0
O7 A:FXX301 2.2 49.3 1.0
CA A:GLY209 3.2 45.6 1.0
C2 A:FXX301 3.4 45.3 1.0
CG1 A:ILE197 3.6 68.7 1.0
C1 A:FXX301 3.9 43.9 1.0
CD1 A:ILE197 4.1 70.5 1.0
C A:GLY209 4.1 45.0 1.0
N A:GLY209 4.2 49.4 1.0
CB A:ALA206 4.4 67.6 1.0
N A:SER210 4.5 42.0 1.0
C3 A:FXX301 4.6 44.4 1.0
CG2 A:ILE197 4.6 67.1 1.0
CB A:ILE197 4.7 67.7 1.0
O A:ALA206 4.7 65.9 1.0
O A:GLY209 4.8 45.6 1.0
OD1 A:ASN213 4.9 43.3 1.0
CD1 A:LEU18 5.0 44.8 1.0

Fluorine binding site 3 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 3 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:50.4
occ:1.00
 F16 A:FXX301 0.0 50.4 1.0
C A:FXX301 1.3 50.7 1.0
F14 A:FXX301 2.1 53.4 1.0
O7 A:FXX301 2.2 49.3 1.0
F13 A:FXX301 2.2 50.7 1.0
C2 A:FXX301 3.2 45.3 1.0
O A:HOH432 3.6 29.8 1.0
CG1 A:ILE197 3.7 68.7 1.0
C3 A:FXX301 3.8 44.4 1.0
C1 A:FXX301 4.3 43.9 1.0
CD1 A:ILE197 4.5 70.5 1.0
CB A:ALA206 4.6 67.6 1.0
CD1 A:LEU200 4.7 65.6 1.0
CA A:GLY192 4.8 53.0 1.0
CB A:ILE197 4.8 67.7 1.0

Fluorine binding site 4 out of 12 in 7ci5

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Fluorine binding site 4 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:49.7
occ:1.00
 F13 B:FXX301 0.0 49.7 1.0
C B:FXX301 1.3 52.0 1.0
F14 B:FXX301 2.2 56.3 1.0
F16 B:FXX301 2.2 57.0 1.0
O7 B:FXX301 2.2 48.2 1.0
C2 B:FXX301 2.7 45.4 1.0
C1 B:FXX301 3.2 44.8 1.0
CB B:ALA214 3.3 47.8 1.0
C3 B:FXX301 3.6 44.5 1.0
CA B:GLY192 3.9 54.2 1.0
CD1 B:ILE197 4.1 58.4 1.0
CG1 B:ILE197 4.1 57.9 1.0
C6 B:FXX301 4.3 46.5 1.0
N B:GLY192 4.6 49.1 1.0
C4 B:FXX301 4.7 44.7 1.0
CA B:GLY209 4.8 50.3 1.0
CA B:ALA214 4.8 50.9 1.0
OD1 B:ASN213 4.8 38.7 1.0
C5 B:FXX301 4.9 46.5 1.0
CG2 B:THR190 4.9 41.5 1.0

Fluorine binding site 5 out of 12 in 7ci5

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Fluorine binding site 5 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:56.3
occ:1.00
 F14 B:FXX301 0.0 56.3 1.0
C B:FXX301 1.3 52.0 1.0
F16 B:FXX301 2.1 57.0 1.0
F13 B:FXX301 2.2 49.7 1.0
O7 B:FXX301 2.2 48.2 1.0
CG1 B:ILE197 3.4 57.9 1.0
C2 B:FXX301 3.5 45.4 1.0
CA B:GLY209 3.5 50.3 1.0
CD1 B:ILE197 3.9 58.4 1.0
C1 B:FXX301 4.1 44.8 1.0
CG2 B:ILE197 4.1 59.8 1.0
CB B:ILE197 4.3 58.7 1.0
C B:GLY209 4.3 49.8 1.0
N B:GLY209 4.4 50.7 1.0
C3 B:FXX301 4.5 44.5 1.0
CB B:ALA206 4.7 71.3 1.0
N B:SER210 4.7 49.1 1.0
O B:ALA206 4.8 65.9 1.0
CD1 B:LEU18 4.9 47.1 1.0
O B:GLY209 5.0 47.9 1.0

Fluorine binding site 6 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 6 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:57.0
occ:1.00
 F16 B:FXX301 0.0 57.0 1.0
C B:FXX301 1.3 52.0 1.0
F14 B:FXX301 2.1 56.3 1.0
O7 B:FXX301 2.2 48.2 1.0
F13 B:FXX301 2.2 49.7 1.0
C2 B:FXX301 3.1 45.4 1.0
C3 B:FXX301 3.5 44.5 1.0
CG1 B:ILE197 3.7 57.9 1.0
C1 B:FXX301 4.3 44.8 1.0
CD1 B:ILE197 4.5 58.4 1.0
CA B:GLY192 4.8 54.2 1.0
CD1 B:LEU200 4.8 75.6 1.0
C4 B:FXX301 4.9 44.7 1.0
CB B:ILE197 4.9 58.7 1.0

Fluorine binding site 7 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 7 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:44.0
occ:1.00
 F13 C:FXX301 0.0 44.0 1.0
C C:FXX301 1.3 42.0 1.0
F14 C:FXX301 2.1 46.8 1.0
F16 C:FXX301 2.2 39.1 1.0
O7 C:FXX301 2.2 40.1 1.0
C2 C:FXX301 2.7 37.8 1.0
C1 C:FXX301 2.9 35.6 1.0
CB C:ALA214 3.6 33.4 1.0
C3 C:FXX301 3.9 35.3 1.0
CD1 C:ILE197 4.1 50.7 1.0
C6 C:FXX301 4.1 33.6 1.0
CA C:GLY209 4.1 42.8 1.0
OD1 C:ASN213 4.3 28.4 1.0
CG1 C:ILE197 4.3 49.3 1.0
N C:SER210 4.6 39.1 1.0
C C:GLY209 4.6 41.8 1.0
CA C:GLY192 4.7 44.3 1.0
C4 C:FXX301 4.9 32.8 1.0
C5 C:FXX301 4.9 32.9 1.0
CD1 C:LEU18 5.0 39.8 1.0

Fluorine binding site 8 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 8 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:46.8
occ:1.00
 F14 C:FXX301 0.0 46.8 1.0
C C:FXX301 1.3 42.0 1.0
F16 C:FXX301 2.1 39.1 1.0
O7 C:FXX301 2.1 40.1 1.0
F13 C:FXX301 2.1 44.0 1.0
C2 C:FXX301 3.4 37.8 1.0
CG1 C:ILE197 3.4 49.3 1.0
CG2 C:ILE197 3.7 46.6 1.0
CD1 C:ILE197 3.9 50.7 1.0
CB C:ALA206 4.1 45.9 1.0
CB C:ILE197 4.1 48.4 1.0
C1 C:FXX301 4.1 35.6 1.0
CA C:GLY209 4.2 42.8 1.0
C3 C:FXX301 4.3 35.3 1.0
CA C:ILE197 4.7 50.8 1.0
CD1 C:LEU18 4.7 39.8 1.0
O C:ALA206 4.8 47.1 1.0
C C:GLY209 4.9 41.8 1.0

Fluorine binding site 9 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 9 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:39.1
occ:1.00
 F16 C:FXX301 0.0 39.1 1.0
C C:FXX301 1.3 42.0 1.0
F14 C:FXX301 2.1 46.8 1.0
F13 C:FXX301 2.2 44.0 1.0
O7 C:FXX301 2.3 40.1 1.0
C2 C:FXX301 3.0 37.8 1.0
C3 C:FXX301 3.4 35.3 1.0
CG1 C:ILE197 3.6 49.3 1.0
C1 C:FXX301 3.9 35.6 1.0
CD1 C:ILE197 3.9 50.7 1.0
CA C:GLY192 4.1 44.3 1.0
C4 C:FXX301 4.6 32.8 1.0
CB C:ILE197 4.8 48.4 1.0
C6 C:FXX301 4.9 33.6 1.0

Fluorine binding site 10 out of 12 in 7ci5

Go back to Fluorine Binding Sites List in 7ci5
Fluorine binding site 10 out of 12 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:36.4
occ:1.00
 F13 D:FXX301 0.0 36.4 1.0
C D:FXX301 1.3 39.4 1.0
F16 D:FXX301 2.1 44.9 1.0
F14 D:FXX301 2.2 41.1 1.0
O7 D:FXX301 2.3 35.7 1.0
C2 D:FXX301 2.8 34.6 1.0
C3 D:FXX301 3.4 32.6 1.0
C1 D:FXX301 3.6 31.5 1.0
CG1 D:ILE197 3.9 51.3 1.0
CA D:GLY192 4.0 42.9 1.0
CD1 D:ILE197 4.1 51.8 1.0
CB D:ALA214 4.4 34.8 1.0
C4 D:FXX301 4.5 29.9 1.0
C6 D:FXX301 4.7 30.8 1.0
N D:GLY192 4.8 40.7 1.0

Reference:

Y.Yamada, H.Takashima, D.L.Walmsley, F.Ushiyama, Y.Matsuda, H.Kanazawa, T.Yamaguchi-Sasaki, N.Tanaka-Yamamoto, J.Yamagishi, R.Kurimoto-Tsuruta, Y.Ogata, N.Ohtake, H.Angove, L.Baker, R.Harris, A.Macias, A.Robertson, A.Surgenor, H.Watanabe, K.Nakano, M.Mima, K.Iwamoto, A.Okada, I.Takata, K.Hitaka, A.Tanaka, K.Fujita, H.Sugiyama, R.E.Hubbard. Fragment-Based Discovery of Novel Non-Hydroxamate Lpxc Inhibitors with Antibacterial Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33210531
DOI: 10.1021/ACS.JMEDCHEM.0C01215
Page generated: Fri Aug 2 06:09:21 2024

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