Fluorine in PDB 4p8l: Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C

The structure of Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C, PDB code: 4p8l was solved by J.Neres, F.Pojer, S.T.Cole, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.10 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.946, 83.149, 80.524, 90.00, 102.79, 90.00
R / Rfree (%)	19.3 / 22.8

The binding sites of Fluorine atom in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C (pdb code 4p8l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C, PDB code: 4p8l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:55.6 occ:1.00 FAW A:36C502 0.0 55.6 1.0 CAV A:36C502 1.3 55.4 1.0 CAU A:36C502 2.4 54.9 1.0 CAY A:36C502 2.4 54.8 1.0 OD1 A:ASN324 2.8 72.7 1.0 CG A:ASN324 2.9 70.2 1.0 ND2 A:ASN324 3.3 67.7 1.0 CAT A:36C502 3.6 53.2 1.0 CB A:ASN324 3.6 72.7 1.0 CAZ A:36C502 3.7 52.9 1.0 CAS A:36C502 4.1 50.6 1.0 O A:LEU317 4.8 62.7 1.0 CB A:LEU317 4.9 62.6 1.0 CA A:ASN324 4.9 72.6 1.0 CD1 A:LEU363 5.0 43.4 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:35.5 occ:1.00 FAJ A:36C502 0.0 35.5 1.0 CAI A:36C502 1.3 33.8 1.0 FAL A:36C502 2.1 36.1 1.0 FAK A:36C502 2.2 34.8 1.0 CAH A:36C502 2.3 32.2 1.0 CAG A:36C502 3.0 30.7 1.0 C A:GLY133 3.2 22.3 1.0 CAM A:36C502 3.3 30.6 1.0 CA A:GLY133 3.5 20.5 1.0 O A:GLY133 3.5 19.9 1.0 N A:LYS134 3.5 23.0 1.0 ND1 A:HIS132 3.7 23.7 1.0 O4 A:FAD501 3.8 23.9 1.0 N A:GLY133 4.1 19.3 1.0 CA A:LYS134 4.2 25.7 1.0 CE1 A:HIS132 4.2 22.8 1.0 CD A:LYS367 4.2 27.2 1.0 CAF A:36C502 4.3 30.4 1.0 O A:HIS132 4.3 19.6 1.0 C A:HIS132 4.4 20.3 1.0 CAN A:36C502 4.5 31.0 1.0 C4 A:FAD501 4.7 24.1 1.0 N3 A:FAD501 4.7 24.0 1.0 CG A:HIS132 4.9 21.9 1.0 CG A:LYS367 4.9 26.9 1.0 CAE A:36C502 4.9 30.4 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:34.8 occ:1.00 FAK A:36C502 0.0 34.8 1.0 CAI A:36C502 1.3 33.8 1.0 FAL A:36C502 2.1 36.1 1.0 FAJ A:36C502 2.2 35.5 1.0 CAH A:36C502 2.3 32.2 1.0 CAM A:36C502 2.7 30.6 1.0 CAG A:36C502 3.6 30.7 1.0 CB A:SER228 3.8 24.9 1.0 CG1 A:VAL365 4.0 31.8 1.0 CAN A:36C502 4.1 31.0 1.0 N A:LYS134 4.2 23.0 1.0 CA A:LYS134 4.3 25.7 1.0 OG A:SER228 4.4 25.2 1.0 CD A:LYS367 4.4 27.2 1.0 CB A:LYS367 4.5 25.3 1.0 C A:GLY133 4.5 22.3 1.0 CB A:LYS134 4.6 27.0 1.0 CAF A:36C502 4.8 30.4 1.0 O4 A:FAD501 4.8 23.9 1.0 O A:GLY133 4.9 19.9 1.0 NAO A:36C502 4.9 30.1 1.0 CAE A:36C502 4.9 30.4 1.0 CG A:LYS367 5.0 26.9 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:36.1 occ:1.00 FAL A:36C502 0.0 36.1 1.0 CAI A:36C502 1.3 33.8 1.0 FAJ A:36C502 2.1 35.5 1.0 FAK A:36C502 2.1 34.8 1.0 CAH A:36C502 2.3 32.2 1.0 CAG A:36C502 2.8 30.7 1.0 CAM A:36C502 3.4 30.6 1.0 CG1 A:VAL365 3.5 31.8 1.0 CB A:LYS367 3.5 25.3 1.0 ND2 A:ASN385 3.6 23.1 1.0 CD A:LYS367 3.8 27.2 1.0 CG A:LYS367 3.8 26.9 1.0 CAF A:36C502 4.1 30.4 1.0 ND1 A:HIS132 4.4 23.7 1.0 CE1 A:HIS132 4.4 22.8 1.0 CAN A:36C502 4.5 31.0 1.0 CG A:ASN385 4.8 22.9 1.0 CAE A:36C502 4.8 30.4 1.0 CA A:LYS367 4.8 23.8 1.0 CE1 A:PHE369 4.8 22.6 1.0 O A:GLY133 4.9 19.9 1.0 CB A:VAL365 5.0 30.8 1.0 C A:GLY133 5.0 22.3 1.0 N A:LYS367 5.0 24.7 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:69.1 occ:1.00 FAW B:36C502 0.0 69.1 1.0 CAV B:36C502 1.3 65.4 1.0 CAU B:36C502 2.4 63.3 1.0 CAY B:36C502 2.4 63.8 1.0 O B:ASN364 3.6 46.4 1.0 CD1 B:TRP230 3.6 46.8 1.0 CAT B:36C502 3.6 61.5 1.0 CAZ B:36C502 3.7 60.8 1.0 N B:ASN364 3.8 43.2 1.0 CA B:LEU363 4.1 48.0 1.0 C B:LEU363 4.1 45.8 1.0 CAS B:36C502 4.1 59.1 1.0 C B:ASN364 4.2 43.5 1.0 CG B:TRP230 4.5 46.1 1.0 CD2 B:LEU363 4.5 51.4 1.0 NE1 B:TRP230 4.5 48.4 1.0 CB B:LEU363 4.6 51.2 1.0 CA B:ASN364 4.6 43.9 1.0 CB B:TRP230 4.6 42.0 1.0 CG2 B:VAL365 4.7 34.6 1.0 O B:LEU363 4.9 44.3 1.0 O B:PHE362 5.0 50.6 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:42.2 occ:1.00 FAJ B:36C502 0.0 42.2 1.0 CAI B:36C502 1.3 40.0 1.0 FAK B:36C502 2.1 42.7 1.0 FAL B:36C502 2.1 39.5 1.0 CAH B:36C502 2.3 39.2 1.0 CAG B:36C502 2.9 38.3 1.0 C B:GLY133 3.2 25.8 1.0 CAM B:36C502 3.4 38.0 1.0 O B:GLY133 3.4 23.7 1.0 CA B:GLY133 3.4 25.2 1.0 ND1 B:HIS132 3.5 28.5 1.0 N B:LYS134 3.6 26.5 1.0 O4 B:FAD501 3.8 31.3 1.0 N B:GLY133 4.0 24.2 1.0 CE1 B:HIS132 4.0 26.1 1.0 CAF B:36C502 4.2 38.1 1.0 CA B:LYS134 4.2 26.9 1.0 O B:HIS132 4.3 25.2 1.0 C B:HIS132 4.4 25.7 1.0 OH B:TYR314 4.4 50.9 1.0 CD B:LYS367 4.5 31.2 1.0 N3 B:FAD501 4.5 30.5 1.0 C4 B:FAD501 4.5 31.6 1.0 CAN B:36C502 4.6 39.9 1.0 CG B:HIS132 4.7 26.9 1.0 CAE B:36C502 4.9 40.0 1.0 CG B:LYS367 4.9 32.3 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:42.7 occ:1.00 FAK B:36C502 0.0 42.7 1.0 CAI B:36C502 1.3 40.0 1.0 FAL B:36C502 2.1 39.5 1.0 FAJ B:36C502 2.1 42.2 1.0 CAH B:36C502 2.4 39.2 1.0 CAM B:36C502 2.7 38.0 1.0 CAG B:36C502 3.6 38.3 1.0 N B:LYS134 3.9 26.5 1.0 CB B:SER228 4.0 31.7 1.0 CA B:LYS134 4.0 26.9 1.0 CAN B:36C502 4.1 39.9 1.0 C B:GLY133 4.2 25.8 1.0 OH B:TYR314 4.2 50.9 1.0 CB B:LYS134 4.3 29.4 1.0 CG1 B:VAL365 4.3 35.3 1.0 OG B:SER228 4.4 31.3 1.0 O4 B:FAD501 4.5 31.3 1.0 O B:GLY133 4.6 23.7 1.0 CG B:LYS134 4.6 30.4 1.0 CD B:LYS367 4.7 31.2 1.0 CA B:GLY133 4.8 25.2 1.0 CE1 B:TYR314 4.8 52.3 1.0 CAF B:36C502 4.8 38.1 1.0 CB B:LYS367 4.9 30.7 1.0 NAO B:36C502 4.9 41.3 1.0 CZ B:TYR314 4.9 52.5 1.0 CAE B:36C502 5.0 40.0 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C


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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor TY36C within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:39.5 occ:1.00 FAL B:36C502 0.0 39.5 1.0 CAI B:36C502 1.3 40.0 1.0 FAK B:36C502 2.1 42.7 1.0 FAJ B:36C502 2.1 42.2 1.0 CAH B:36C502 2.3 39.2 1.0 CAG B:36C502 2.9 38.3 1.0 CAM B:36C502 3.4 38.0 1.0 CG1 B:VAL365 3.4 35.3 1.0 CB B:LYS367 3.5 30.7 1.0 ND2 B:ASN385 3.8 33.4 1.0 CG B:LYS367 3.8 32.3 1.0 CD B:LYS367 4.0 31.2 1.0 CAF B:36C502 4.3 38.1 1.0 CAN B:36C502 4.6 39.9 1.0 ND1 B:HIS132 4.6 28.5 1.0 CE1 B:HIS132 4.7 26.1 1.0 CB B:SER228 4.7 31.7 1.0 O B:GLY133 4.8 23.7 1.0 CB B:VAL365 4.8 36.6 1.0 CAE B:36C502 4.9 40.0 1.0 C B:GLY133 4.9 25.8 1.0 CA B:LYS367 5.0 31.2 1.0 CG B:ASN385 5.0 31.9 1.0

J.Neres, R.C.Hartkoorn, L.R.Chiarelli, R.Gadupudi, M.R.Pasca, G.Mori, D.Farina, S.Savina, V.Makarov, G.S.Kolly, E.Molteni, C.Binda, N.Dhar, S.Ferrari, P.Brodin, V.Delorme, V.Landry, A.L.Ribeiro, A.Venturelli, P.Saxena, F.Pojer, A.Carta, R.Luciani, A.Porta, G.Zanoni, E.De Rossi, M.P.Costi, G.Riccardi, S.T.Cole. 2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Non-Covalent Inhibition of DPRE1. Acs Chem.Biol. 2014.
ISSN: ESSN 1554-8937
PubMed: 25427196
DOI: 10.1021/CB5007163