Chlorine in PDB 5nr7: Mtb Tmk Crystal Structure in Complex with Compound 43

All present enzymatic activity of Mtb Tmk Crystal Structure in Complex with Compound 43:
2.7.4.9;

The structure of Mtb Tmk Crystal Structure in Complex with Compound 43, PDB code: 5nr7 was solved by R.Merceron, L.Song, H.Munier-Lehmann, S.Van Calenbergh, S.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 2.35
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	73.630, 73.630, 72.860, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.6

The binding sites of Chlorine atom in the Mtb Tmk Crystal Structure in Complex with Compound 43 (pdb code 5nr7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Mtb Tmk Crystal Structure in Complex with Compound 43, PDB code: 5nr7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Mtb Tmk Crystal Structure in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mtb Tmk Crystal Structure in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:98.5 occ:1.00 CL A:YUI301 0.0 98.5 1.0 C14 A:YUI301 1.7 95.1 1.0 C15 A:YUI301 2.7 91.8 1.0 C13 A:YUI301 2.7 94.0 1.0 H16 A:YUI301 2.8 0.2 0.0 H15 A:YUI301 2.8 0.8 0.0 C10 A:YUI301 4.0 88.6 1.0 C12 A:YUI301 4.0 92.5 1.0 CG A:TYR39 4.3 43.2 1.0 CD2 A:TYR39 4.3 39.8 1.0 CB A:ALA49 4.4 47.3 1.0 C11 A:YUI301 4.5 90.9 1.0 CB A:TYR39 4.6 45.6 1.0 CD1 A:TYR39 4.7 42.3 1.0 CE2 A:TYR39 4.8 38.9 1.0 H14 A:YUI301 4.8 0.0 0.0

Chlorine binding site 2 out of 4 in the Mtb Tmk Crystal Structure in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mtb Tmk Crystal Structure in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:48.6 occ:1.00 O A:HOH425 3.0 45.0 1.0 N A:GLY12 3.2 42.0 1.0 N A:LYS13 3.3 34.8 1.0 N A:GLY10 3.4 41.7 1.0 NZ A:LYS13 3.6 41.9 1.0 N A:ALA11 3.6 40.4 1.0 CE A:LYS13 3.8 40.4 1.0 O A:VAL8 3.9 39.1 1.0 CA A:GLY12 3.9 39.4 1.0 CB A:LYS13 3.9 32.9 1.0 C A:GLY10 4.0 43.1 1.0 CA A:GLY10 4.0 42.6 1.0 CG A:LYS13 4.1 36.4 1.0 C A:GLY12 4.1 35.3 1.0 C A:ALA11 4.2 41.7 1.0 CA A:LYS13 4.2 33.1 1.0 C A:ASP9 4.2 44.8 1.0 CA A:ALA11 4.3 39.0 1.0 CA A:ASP9 4.3 47.4 1.0 O A:HOH408 4.4 37.2 1.0 CB A:ALA11 4.5 36.5 1.0 CD A:LYS13 4.6 38.7 1.0 N A:ARG14 4.8 36.9 1.0 C A:VAL8 4.8 39.6 1.0 O A:GLY10 4.9 43.7 1.0

Chlorine binding site 3 out of 4 in the Mtb Tmk Crystal Structure in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mtb Tmk Crystal Structure in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:0.0 occ:1.00 CL B:YUI301 0.0 0.0 1.0 C14 B:YUI301 1.7 0.4 1.0 C15 B:YUI301 2.7 0.8 1.0 C13 B:YUI301 2.7 0.4 1.0 H16 B:YUI301 2.8 0.5 0.0 H15 B:YUI301 2.8 0.7 0.0 CB B:ALA49 4.0 63.9 1.0 C10 B:YUI301 4.0 0.8 1.0 C12 B:YUI301 4.0 0.3 1.0 CD2 B:TYR39 4.0 58.3 1.0 CG B:TYR39 4.0 59.8 1.0 CE2 B:TYR39 4.4 58.0 1.0 CB B:TYR39 4.4 61.3 1.0 CD1 B:TYR39 4.4 59.2 1.0 C11 B:YUI301 4.5 0.5 1.0 CZ B:TYR39 4.7 59.3 1.0 CE1 B:TYR39 4.7 59.4 1.0 H14 B:YUI301 4.8 0.4 0.0

Chlorine binding site 4 out of 4 in the Mtb Tmk Crystal Structure in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mtb Tmk Crystal Structure in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:68.4 occ:1.00 N B:LYS13 3.2 52.2 1.0 N B:GLY12 3.2 64.2 1.0 NZ B:LYS13 3.4 55.4 1.0 N B:GLY10 3.5 79.4 1.0 N B:ALA11 3.7 70.7 1.0 CA B:GLY12 3.8 59.1 1.0 CB B:LYS13 3.8 47.5 1.0 CE B:LYS13 3.9 52.5 1.0 C B:GLY12 3.9 54.9 1.0 C B:GLY10 4.0 74.2 1.0 CA B:GLY10 4.1 79.4 1.0 CA B:LYS13 4.1 49.6 1.0 CG B:LYS13 4.1 48.1 1.0 O B:VAL8 4.1 67.1 1.0 C B:ALA11 4.2 67.2 1.0 CA B:ALA11 4.4 68.2 1.0 N B:ARG14 4.4 53.2 1.0 C B:ASP9 4.4 80.2 1.0 CA B:ASP9 4.5 78.6 1.0 O B:HOH413 4.5 46.4 1.0 CB B:ALA11 4.6 66.6 1.0 CD B:LYS13 4.6 47.7 1.0 C B:LYS13 4.8 52.0 1.0 O B:GLY10 4.9 74.1 1.0

L.Song, R.Merceron, B.Gracia, A.L.Quintana, M.D.P.Risseeuw, F.Hulpia, P.Cos, J.A.Ainsa, H.Munier-Lehmann, S.N.Savvides, S.Van Calenbergh. Structure Guided Lead Generation Toward Nonchiral M. Tuberculosis Thymidylate Kinase Inhibitors. J. Med. Chem. V. 61 2753 2018.
ISSN: ISSN 1520-4804
PubMed: 29510037
DOI: 10.1021/ACS.JMEDCHEM.7B01570