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Chlorine in PDB 6waa: K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)

Enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)

All present enzymatic activity of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One):
5.6.2.2;

Protein crystallography data

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa 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) 82.08 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.590, 157.481, 144.060, 90.00, 94.93, 90.00
R / Rfree (%) 27.4 / 30.1

Other elements in 6waa:

The structure of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) (pdb code 6waa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One), PDB code: 6waa:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6waa

Go back to Chlorine Binding Sites List in 6waa
Chlorine binding site 1 out of 2 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1505

b:64.5
occ:1.00
 HH12 B:ARG1365 2.3 59.3 1.0
NH1 B:ARG1365 3.0 56.3 1.0
HH22 B:ARG1365 3.1 57.4 1.0
HH11 B:ARG1365 3.5 59.3 1.0
HD3 B:ARG1372 3.6 49.2 1.0
NH2 B:ARG1365 3.6 56.5 1.0
CZ B:ARG1365 3.7 56.4 1.0
HD21 B:LEU1440 4.0 60.7 1.0
HD2 B:ARG1372 4.2 49.2 1.0
HB3 B:LYS1368 4.3 70.6 1.0
CD B:ARG1372 4.4 54.3 1.0
HH21 B:ARG1365 4.4 57.4 1.0
HB2 B:ARG1372 4.7 51.2 1.0
HD22 B:LEU1440 4.8 60.7 1.0
HG22 B:VAL1369 4.9 47.5 1.0
CD2 B:LEU1440 4.9 56.6 1.0
NE B:ARG1365 4.9 56.5 1.0
HD11 B:LEU1440 5.0 61.9 1.0
HA B:VAL1369 5.0 48.7 1.0

Chlorine binding site 2 out of 2 in 6waa

Go back to Chlorine Binding Sites List in 6waa
Chlorine binding site 2 out of 2 in the K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of K. Pneumoniae Topoisomerase IV (Pare-Parc) in Complex with Dna and Compound 34 (7-[(1S,5R)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3-Yl]-4- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2(1H)-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1504

b:62.7
occ:1.00
 HH12 H:ARG1365 3.1 63.2 1.0
HG2 H:ARG1372 3.7 46.6 1.0
NH1 H:ARG1365 3.8 66.8 1.0
HB2 H:ARG1372 3.8 71.0 1.0
HH11 H:ARG1365 4.1 63.2 1.0
HH22 H:ARG1365 4.2 51.6 1.0
HD21 H:LEU1440 4.2 66.8 1.0
HD3 H:ARG1372 4.3 45.1 1.0
CG H:ARG1372 4.4 65.9 1.0
HB3 H:LYS1368 4.4 65.0 1.0
CB H:ARG1372 4.4 67.6 1.0
HB3 H:ARG1372 4.5 71.0 1.0
CZ H:ARG1365 4.7 67.0 1.0
O H:LYS1368 4.7 70.1 1.0
NH2 H:ARG1365 4.7 67.4 1.0
HD11 H:LEU1440 4.8 61.2 1.0
CD H:ARG1372 4.8 66.1 1.0
HD22 H:LEU1440 4.9 66.8 1.0
HA H:VAL1369 4.9 59.5 1.0
CD2 H:LEU1440 5.0 73.0 1.0

Reference:

C.K.Skepper, D.Armstrong, C.J.Balibar, D.Bauer, C.Bellamacina, B.M.Benton, D.Bussiere, G.De Pascale, J.De Vicente, C.R.Dean, B.Dhumale, L.M.Fisher, J.Fuller, M.Fulsunder, L.M.Holder, C.Hu, B.Kantariya, G.Lapointe, J.A.Leeds, X.Li, P.Lu, A.Lvov, S.Ma, S.Madhavan, S.Malekar, D.Mckenney, W.Mergo, L.Metzger, H.E.Moser, D.Mutnick, J.Noeske, C.Osborne, A.Patel, D.Patel, T.Patel, K.Prajapati, K.R.Prosen, F.Reck, D.L.Richie, A.Rico, M.R.Sanderson, S.Satasia, W.S.Sawyer, J.Selvarajah, N.Shah, K.Shanghavi, W.Shu, K.V.Thompson, M.Traebert, A.Vala, L.Vala, D.A.Veselkov, J.Vo, M.Wang, M.Widya, S.L.Williams, Y.Xu, Q.Yue, R.Zang, B.Zhou, A.Rivkin. Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J.Med.Chem. V. 63 7773 2020.
ISSN: ISSN 0022-2623
PubMed: 32634310
DOI: 10.1021/ACS.JMEDCHEM.0C00347
Page generated: Sat Jul 12 21:14:01 2025

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