Fluorine in PDB 7lhz: K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)

Enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)

All present enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25):
5.6.2.2;

Protein crystallography data

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25), PDB code: 7lhz was solved by J.Noeske, W.Shu, C.Bellamacina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.92 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.185, 159.818, 144.059, 90, 94.94, 90
R / Rfree (%) 28.3 / 30.8

Other elements in 7lhz:

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) (pdb code 7lhz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25), PDB code: 7lhz:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7lhz

Go back to Fluorine Binding Sites List in 7lhz
Fluorine binding site 1 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F601

b:93.2
occ:1.00
F8 K:Y21601 0.0 93.2 1.0
C1 K:Y21601 1.3 92.8 1.0
C6 K:Y21601 2.3 91.3 1.0
C2 K:Y21601 2.4 93.4 1.0
N9 K:Y21601 2.8 93.4 1.0
C18 K:Y21601 2.8 92.9 1.0
C4 K:DC515 3.1 93.7 1.0
N3 K:DC515 3.1 95.0 1.0
H62 K:DA516 3.2 79.5 1.0
N6 K:DA516 3.3 88.0 1.0
C6 K:DA516 3.3 87.9 1.0
C5 K:DA516 3.3 89.3 1.0
N7 K:DA516 3.4 91.3 1.0
C2 K:DC515 3.4 94.1 1.0
C5 K:DC515 3.5 93.4 1.0
H1 I:DG712 3.5 85.6 1.0
N4 K:DC515 3.6 93.6 1.0
C5 K:Y21601 3.6 91.8 1.0
C3 K:Y21601 3.6 93.5 1.0
H22 I:DG712 3.7 86.6 1.0
H61 K:DA516 3.7 79.5 1.0
N1 K:DC515 3.7 94.2 1.0
C6 K:DC515 3.8 94.2 1.0
H42 K:DC515 3.8 82.9 1.0
N1 I:DG712 3.9 93.2 1.0
H5 K:DC515 3.9 87.3 1.0
C21 K:Y21601 4.0 93.6 1.0
H41 K:DC515 4.0 82.9 1.0
N1 K:DA516 4.1 87.2 1.0
N2 I:DG712 4.1 92.4 1.0
C4 K:DA516 4.1 89.5 1.0
O2 K:DC515 4.1 92.6 1.0
C4 K:Y21601 4.1 92.8 1.0
C8 K:DA516 4.2 92.7 1.0
C19 K:Y21601 4.2 93.5 1.0
C2 I:DG712 4.3 92.8 1.0
H6 K:DC515 4.4 88.8 1.0
H2' K:DC515 4.5 91.2 1.0
C20 K:Y21601 4.5 93.9 1.0
N9 K:DA516 4.6 91.5 1.0
H21 I:DG712 4.6 86.6 1.0
C2 K:DA516 4.7 87.5 1.0
H8 K:DA516 4.7 87.9 1.0
C6 I:DG712 4.7 92.9 1.0
C1' K:DC515 4.8 95.2 1.0
H1' K:DC515 4.8 89.2 1.0
N3 K:DA516 4.8 88.5 1.0
O10 K:Y21601 4.8 94.0 1.0
C7 K:Y21601 4.9 90.9 1.0
O6 I:DG712 4.9 91.1 1.0

Fluorine binding site 2 out of 4 in 7lhz

Go back to Fluorine Binding Sites List in 7lhz
Fluorine binding site 2 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F801

b:83.7
occ:1.00
F8 I:Y21801 0.0 83.7 1.0
C1 I:Y21801 1.3 82.6 1.0
C2 I:Y21801 2.4 82.2 1.0
C6 I:Y21801 2.4 82.1 1.0
N9 I:Y21801 2.7 82.3 1.0
C18 I:Y21801 3.0 82.8 1.0
C2 I:DC715 3.1 83.3 1.0
N3 I:DC715 3.1 85.1 1.0
C5 I:DA716 3.3 76.9 1.0
C6 I:DA716 3.3 77.1 1.0
N1 I:DC715 3.4 82.3 1.0
C4 I:DC715 3.4 85.7 1.0
H2' I:DC715 3.4 73.8 1.0
N7 I:DA716 3.5 79.5 1.0
O2 I:DC715 3.6 82.8 1.0
N6 I:DA716 3.6 80.9 1.0
H62 I:DA716 3.6 67.1 1.0
C3 I:Y21801 3.6 81.6 1.0
C6 I:DC715 3.6 82.6 1.0
C5 I:Y21801 3.6 81.8 1.0
C5 I:DC715 3.7 84.2 1.0
C21 I:Y21801 3.8 81.4 1.0
H22 K:DG512 3.8 81.0 1.0
H1 K:DG512 3.8 75.5 1.0
C4 I:DA716 3.8 73.8 1.0
N1 I:DA716 3.9 73.6 1.0
H61 I:DA716 4.0 67.1 1.0
C4 I:Y21801 4.1 81.5 1.0
C8 I:DA716 4.1 77.8 1.0
N4 I:DC715 4.1 87.8 1.0
C1' I:DC715 4.2 81.1 1.0
C2' I:DC715 4.2 77.1 1.0
N2 K:DG512 4.2 100.1 1.0
H6 I:DC715 4.2 76.2 1.0
N1 K:DG512 4.2 82.5 1.0
H5 I:DC715 4.3 76.5 1.0
H1' I:DC715 4.3 76.0 1.0
N9 I:DA716 4.3 74.7 1.0
C2 I:DA716 4.4 70.9 1.0
H42 I:DC715 4.4 77.1 1.0
C19 I:Y21801 4.4 82.6 1.0
N3 I:DA716 4.4 71.0 1.0
C20 I:Y21801 4.4 82.0 1.0
C2 K:DG512 4.5 91.6 1.0
H2'' I:DC715 4.6 73.8 1.0
H41 I:DC715 4.6 77.1 1.0
H8 I:DA716 4.7 67.1 1.0
H21 K:DG512 4.7 81.0 1.0
O10 I:Y21801 4.8 80.7 1.0
C7 I:Y21801 4.9 81.0 1.0

Fluorine binding site 3 out of 4 in 7lhz

Go back to Fluorine Binding Sites List in 7lhz
Fluorine binding site 3 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F401

b:88.5
occ:1.00
F8 G:Y21401 0.0 88.5 1.0
C1 G:Y21401 1.3 87.0 1.0
C6 G:Y21401 2.4 86.2 1.0
C2 G:Y21401 2.4 86.0 1.0
N9 G:Y21401 2.8 86.0 1.0
C18 G:Y21401 2.8 86.7 1.0
H62 G:DA316 2.9 70.6 1.0
N6 G:DA316 3.0 77.2 1.0
C4 G:DC315 3.0 86.5 1.0
C6 G:DA316 3.0 73.3 1.0
C5 G:DA316 3.1 73.4 1.0
N3 G:DC315 3.1 83.4 1.0
N7 G:DA316 3.2 77.4 1.0
C5 G:DC315 3.3 89.2 1.0
C2 G:DC315 3.3 82.3 1.0
H61 G:DA316 3.5 70.6 1.0
C6 G:DC315 3.5 87.3 1.0
N1 G:DC315 3.5 83.7 1.0
N4 G:DC315 3.6 87.8 1.0
C5 G:Y21401 3.6 85.5 1.0
C3 G:Y21401 3.6 84.9 1.0
H5 G:DC315 3.7 82.2 1.0
H2' G:DC315 3.8 75.5 1.0
H42 G:DC315 3.9 82.5 1.0
N1 G:DA316 3.9 69.8 1.0
C4 G:DA316 3.9 69.9 1.0
H41 G:DC315 4.0 82.5 1.0
C8 G:DA316 4.0 75.0 1.0
C21 G:Y21401 4.0 84.7 1.0
O2 G:DC315 4.1 80.8 1.0
H22 F:DG112 4.1 83.4 1.0
H6 G:DC315 4.1 80.8 1.0
C4 G:Y21401 4.1 84.8 1.0
C19 G:Y21401 4.3 86.4 1.0
H1 F:DG112 4.4 80.5 1.0
N9 G:DA316 4.4 70.8 1.0
C2 G:DA316 4.5 67.5 1.0
H8 G:DA316 4.5 68.7 1.0
C1' G:DC315 4.6 82.3 1.0
C2' G:DC315 4.6 78.6 1.0
N2 F:DG112 4.6 85.3 1.0
N3 G:DA316 4.7 67.4 1.0
C20 G:Y21401 4.7 85.4 1.0
O10 G:Y21401 4.8 83.6 1.0
H1' G:DC315 4.9 77.6 1.0
C7 G:Y21401 4.9 84.7 1.0
N1 F:DG112 4.9 83.0 1.0

Fluorine binding site 4 out of 4 in 7lhz

Go back to Fluorine Binding Sites List in 7lhz
Fluorine binding site 4 out of 4 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and (3S)-10-[(3R)-3-(1-Aminocyclopropyl)Pyrrolidin-1-Yl]-9-Fluoro-3- Methyl-5-Oxo-2,3-Dihydro-5H-[1,4]Oxazino[2,3,4-Ij]Quinoline-6- Carboxylic Acid (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:102.0
occ:1.00
F8 F:Y21201 0.0 102.0 1.0
C1 F:Y21201 1.3 101.9 1.0
C6 F:Y21201 2.4 100.8 1.0
C2 F:Y21201 2.4 102.9 1.0
N9 F:Y21201 2.8 103.4 1.0
C18 F:Y21201 2.9 103.3 1.0
C4 F:DC115 3.0 102.5 1.0
C5 F:DA116 3.1 103.9 1.0
C6 F:DA116 3.1 102.4 1.0
C5 F:DC115 3.2 103.8 1.0
N3 F:DC115 3.3 101.4 1.0
N4 F:DC115 3.3 102.2 1.0
N6 F:DA116 3.4 104.7 1.0
N7 F:DA116 3.5 107.8 1.0
H5 F:DC115 3.5 96.5 1.0
C4 F:DA116 3.6 100.7 1.0
H62 F:DA116 3.6 92.7 1.0
H22 G:DG312 3.6 90.3 1.0
H41 F:DC115 3.6 92.7 1.0
N1 F:DA116 3.6 98.0 1.0
C5 F:Y21201 3.6 101.6 1.0
C3 F:Y21201 3.6 103.3 1.0
C19 F:Y21201 3.6 103.7 1.0
H42 F:DC115 3.7 92.7 1.0
C6 F:DC115 3.7 104.1 1.0
C2 F:DC115 3.8 101.0 1.0
H61 F:DA116 3.9 92.7 1.0
C21 F:Y21201 3.9 103.4 1.0
N2 G:DG312 3.9 101.3 1.0
N1 F:DC115 3.9 102.5 1.0
C2 F:DA116 4.0 95.0 1.0
C8 F:DA116 4.0 107.2 1.0
N3 F:DA116 4.1 95.9 1.0
H1 G:DG312 4.1 87.5 1.0
C4 F:Y21201 4.1 102.8 1.0
N9 F:DA116 4.1 103.0 1.0
C20 F:Y21201 4.2 103.7 1.0
H6 F:DC115 4.2 98.0 1.0
H21 G:DG312 4.2 90.3 1.0
H2' F:DC115 4.3 99.3 1.0
C2 G:DG312 4.4 99.6 1.0
N1 G:DG312 4.4 97.6 1.0
O2 F:DC115 4.6 98.8 1.0
H2 F:DA116 4.6 90.6 1.0
H8 F:DA116 4.7 98.2 1.0
O10 F:Y21201 4.8 103.8 1.0
C7 F:Y21201 4.9 100.2 1.0

Reference:

G.Lapointe, C.K.Skepper, L.M.Holder, D.Armstrong, C.Bellamacina, J.Blais, D.Bussiere, J.Bian, C.Cepura, H.Chan, C.R.Dean, G.De Pascale, B.Dhumale, L.M.Fisher, M.Fulsunder, B.Kantariya, J.Kim, S.King, L.Kossy, U.Kulkarni, J.Lakshman, J.A.Leeds, X.Ling, A.Lvov, S.Ma, S.Malekar, D.Mckenney, W.Mergo, L.Metzger, K.Mhaske, H.E.Moser, M.Mostafavi, S.Namballa, J.Noeske, C.Osborne, A.Patel, D.Patel, T.Patel, P.Piechon, V.Polyakov, K.Prajapati, K.R.Prosen, F.Reck, D.L.Richie, M.R.Sanderson, S.Satasia, B.Savani, J.Selvarajah, V.Sethuraman, W.Shu, K.Tashiro, K.V.Thompson, K.Vaarla, L.Vala, D.A.Veselkov, J.Vo, B.Vora, T.Wagner, L.Wedel, S.L.Williams, S.Yendluri, Q.Yue, A.Yifru, Y.Zhang, A.Rivkin. Discovery and Optimization of Dna Gyrase and Topoisomerase IV Inhibitors with Potent Activity Against Fluoroquinolone-Resistant Gram-Positive Bacteria. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33929852
DOI: 10.1021/ACS.JMEDCHEM.1C00375
Page generated: Sat Jul 10 14:17:58 2021

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