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Fluorine in PDB 7ci4: 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: 7ci4 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) 23.32 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.367, 51.180, 96.763, 90.00, 108.22, 90.00
R / Rfree (%) 18.7 / 24.1

Other elements in 7ci4:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7ci4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 1 out of 6 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:F1300

b:41.7
occ:1.00
 F16 A:FXU1300 0.0 41.7 1.0
C15 A:FXU1300 1.3 40.0 1.0
F18 A:FXU1300 2.1 44.3 1.0
F17 A:FXU1300 2.2 41.8 1.0
O14 A:FXU1300 2.3 32.1 1.0
C2 A:FXU1300 2.9 27.0 1.0
C1 A:FXU1300 3.0 26.0 1.0
CD1 A:ILE197 3.6 33.6 1.0
CB A:ALA214 3.7 23.1 1.0
CA A:GLY209 3.8 30.2 1.0
OD1 A:ASN213 3.9 20.2 1.0
N A:SER210 4.1 33.1 1.0
C3 A:FXU1300 4.1 25.9 1.0
CG1 A:ILE197 4.1 33.6 1.0
C A:GLY209 4.2 32.8 1.0
C6 A:FXU1300 4.3 28.2 1.0
CA A:GLY192 4.6 26.7 1.0
O A:SER210 4.6 30.1 1.0
CD1 A:LEU18 4.7 30.2 1.0
CA A:ALA214 5.0 23.7 1.0

Fluorine binding site 2 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 2 out of 6 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:F1300

b:41.8
occ:1.00
 F17 A:FXU1300 0.0 41.8 1.0
C15 A:FXU1300 1.3 40.0 1.0
F18 A:FXU1300 2.2 44.3 1.0
O14 A:FXU1300 2.2 32.1 1.0
F16 A:FXU1300 2.2 41.7 1.0
CG1 A:ILE197 3.1 33.6 1.0
C2 A:FXU1300 3.5 27.0 1.0
CD1 A:ILE197 3.5 33.6 1.0
CB A:ALA206 4.1 32.2 1.0
CB A:ILE197 4.2 31.2 1.0
CG2 A:ILE197 4.3 30.6 1.0
C1 A:FXU1300 4.3 26.0 1.0
C3 A:FXU1300 4.3 25.9 1.0
CA A:GLY209 4.5 30.2 1.0
CA A:ILE197 4.7 29.3 1.0
CD1 A:LEU18 4.7 30.2 1.0
CD1 A:LEU200 4.8 38.3 1.0

Fluorine binding site 3 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 3 out of 6 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:F1300

b:44.3
occ:1.00
 F18 A:FXU1300 0.0 44.3 1.0
C15 A:FXU1300 1.3 40.0 1.0
F16 A:FXU1300 2.1 41.7 1.0
F17 A:FXU1300 2.2 41.8 1.0
O14 A:FXU1300 2.3 32.1 1.0
C2 A:FXU1300 2.9 27.0 1.0
CA A:GLY192 3.4 26.7 1.0
C3 A:FXU1300 3.5 25.9 1.0
CD1 A:ILE197 3.6 33.6 1.0
CG1 A:ILE197 3.7 33.6 1.0
C1 A:FXU1300 3.7 26.0 1.0
O A:HOH1536 4.0 29.0 1.0
CB A:ALA214 4.1 23.1 1.0
N A:GLY192 4.3 26.6 1.0
O A:PHE191 4.6 24.6 1.0
C A:GLY192 4.6 24.6 1.0
C4 A:FXU1300 4.7 26.1 1.0
C A:PHE191 4.8 24.3 1.0
C6 A:FXU1300 4.8 28.2 1.0
N A:PHE193 4.9 25.1 1.0

Fluorine binding site 4 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 4 out of 6 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:F1300

b:45.3
occ:1.00
 F16 B:FXU1300 0.0 45.3 1.0
C15 B:FXU1300 1.3 44.6 1.0
O14 B:FXU1300 2.1 34.4 1.0
F18 B:FXU1300 2.2 46.8 1.0
F17 B:FXU1300 2.2 50.3 1.0
CG1 B:ILE197 3.2 35.2 1.0
CD1 B:ILE197 3.4 36.0 1.0
C2 B:FXU1300 3.4 31.2 1.0
CG2 B:ILE197 3.9 36.6 1.0
CB B:ALA206 4.0 30.8 1.0
CB B:ILE197 4.1 36.0 1.0
C1 B:FXU1300 4.2 29.1 1.0
CA B:GLY209 4.2 32.4 1.0
C3 B:FXU1300 4.4 31.0 1.0
CD1 B:LEU18 4.6 33.8 1.0
C B:GLY209 4.7 33.8 1.0
CA B:ILE197 4.7 34.6 1.0
CD1 B:LEU200 4.9 41.0 1.0

Fluorine binding site 5 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 5 out of 6 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:F1300

b:50.3
occ:1.00
 F17 B:FXU1300 0.0 50.3 1.0
C15 B:FXU1300 1.3 44.6 1.0
F18 B:FXU1300 2.2 46.8 1.0
F16 B:FXU1300 2.2 45.3 1.0
O14 B:FXU1300 2.2 34.4 1.0
C2 B:FXU1300 2.9 31.2 1.0
C3 B:FXU1300 3.4 31.0 1.0
CG1 B:ILE197 3.7 35.2 1.0
CD1 B:ILE197 3.7 36.0 1.0
CA B:GLY192 3.9 35.8 1.0
C1 B:FXU1300 3.9 29.1 1.0
C4 B:FXU1300 4.6 26.4 1.0
N B:GLY192 4.7 34.2 1.0
CB B:ALA214 4.8 27.1 1.0
O B:PHE191 4.9 34.0 1.0
C6 B:FXU1300 5.0 29.2 1.0

Fluorine binding site 6 out of 6 in 7ci4

Go back to Fluorine Binding Sites List in 7ci4
Fluorine binding site 6 out of 6 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:F1300

b:46.8
occ:1.00
 F18 B:FXU1300 0.0 46.8 1.0
C15 B:FXU1300 1.3 44.6 1.0
F17 B:FXU1300 2.2 50.3 1.0
F16 B:FXU1300 2.2 45.3 1.0
O14 B:FXU1300 2.2 34.4 1.0
C2 B:FXU1300 2.8 31.2 1.0
C1 B:FXU1300 3.0 29.1 1.0
CD1 B:ILE197 3.5 36.0 1.0
CB B:ALA214 3.5 27.1 1.0
C3 B:FXU1300 3.9 31.0 1.0
CG1 B:ILE197 4.1 35.2 1.0
C6 B:FXU1300 4.2 29.2 1.0
CA B:GLY209 4.3 32.4 1.0
OD1 B:ASN213 4.3 22.0 1.0
N B:SER210 4.3 35.4 1.0
C B:GLY209 4.6 33.8 1.0
CA B:GLY192 4.7 35.8 1.0
O B:SER210 4.8 33.2 1.0
CA B:ALA214 4.9 26.5 1.0
C4 B:FXU1300 4.9 26.4 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 06:09:02 2024

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