Fluorine in PDB 4p8t: Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129

The structure of Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129, PDB code: 4p8t 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)	49.50 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.231, 83.039, 80.729, 90.00, 102.84, 90.00
R / Rfree (%)	18.5 / 23.7

The binding sites of Fluorine atom in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129 (pdb code 4p8t). 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 M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129, PDB code: 4p8t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:37.9 occ:1.00 FAL A:R26502 0.0 37.9 1.0 CAI A:R26502 1.3 38.6 1.0 FAJ A:R26502 2.1 41.8 1.0 FAK A:R26502 2.2 39.9 1.0 CAH A:R26502 2.3 37.1 1.0 CAM A:R26502 2.7 36.8 1.0 CAG A:R26502 3.6 36.3 1.0 CG1 A:VAL365 3.6 35.9 1.0 CB A:SER228 3.6 29.4 1.0 OG A:SER228 4.1 31.6 1.0 CAN A:R26502 4.1 36.3 1.0 C7 A:2J3504 4.2 64.9 1.0 CD A:LYS367 4.4 27.2 1.0 CA A:LYS134 4.4 26.8 1.0 O4 A:2J3504 4.4 64.5 1.0 CB A:LYS367 4.4 26.1 1.0 N A:LYS134 4.5 25.6 1.0 C14 A:2J3504 4.6 62.4 1.0 C A:GLY133 4.7 25.4 1.0 CAF A:R26502 4.7 35.8 1.0 CB A:LYS134 4.8 27.5 1.0 C6 A:2J3504 4.8 67.3 1.0 CG A:LYS134 4.8 29.8 1.0 C8 A:2J3504 4.9 64.1 1.0 O A:GLY133 4.9 25.7 1.0 CAE A:R26502 5.0 36.2 1.0 CB A:VAL365 5.0 33.8 1.0 CG A:LYS367 5.0 27.1 1.0 NAO A:R26502 5.0 36.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:41.8 occ:1.00 FAJ A:R26502 0.0 41.8 1.0 CAI A:R26502 1.3 38.6 1.0 FAK A:R26502 2.1 39.9 1.0 FAL A:R26502 2.1 37.9 1.0 CAH A:R26502 2.3 37.1 1.0 CAG A:R26502 2.8 36.3 1.0 CB A:LYS367 3.5 26.1 1.0 CAM A:R26502 3.5 36.8 1.0 CG1 A:VAL365 3.5 35.9 1.0 ND2 A:ASN385 3.7 26.3 1.0 CD A:LYS367 3.7 27.2 1.0 CG A:LYS367 3.9 27.1 1.0 CAF A:R26502 4.1 35.8 1.0 CD2 A:HIS132 4.3 24.6 1.0 NE2 A:HIS132 4.6 24.3 1.0 CAN A:R26502 4.7 36.3 1.0 CE1 A:PHE369 4.8 25.8 1.0 CG A:ASN385 4.8 25.4 1.0 CA A:LYS367 4.8 26.4 1.0 O A:GLY133 4.9 25.7 1.0 CAE A:R26502 4.9 36.2 1.0 CB A:VAL365 4.9 33.8 1.0 CB A:SER228 4.9 29.4 1.0 N A:LYS367 5.0 26.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:39.9 occ:1.00 FAK A:R26502 0.0 39.9 1.0 CAI A:R26502 1.3 38.6 1.0 FAJ A:R26502 2.1 41.8 1.0 FAL A:R26502 2.2 37.9 1.0 CAH A:R26502 2.3 37.1 1.0 CAG A:R26502 3.0 36.3 1.0 C A:GLY133 3.2 25.4 1.0 CAM A:R26502 3.3 36.8 1.0 O A:GLY133 3.4 25.7 1.0 N A:LYS134 3.6 25.6 1.0 CA A:GLY133 3.6 25.1 1.0 CD2 A:HIS132 3.7 24.6 1.0 CA A:LYS134 4.0 26.8 1.0 O4 A:FAD501 4.0 27.8 1.0 CD A:LYS367 4.1 27.2 1.0 N A:GLY133 4.2 25.1 1.0 CAF A:R26502 4.3 35.8 1.0 NE2 A:HIS132 4.4 24.3 1.0 O A:HIS132 4.5 25.4 1.0 CAN A:R26502 4.5 36.3 1.0 C A:HIS132 4.6 25.1 1.0 C4 A:FAD501 4.9 26.4 1.0 CG A:HIS132 4.9 24.4 1.0 CAE A:R26502 4.9 36.2 1.0 N3 A:FAD501 4.9 25.8 1.0 CB A:LYS134 4.9 27.5 1.0 CG A:LYS367 5.0 27.1 1.0 CB A:LYS367 5.0 26.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:46.5 occ:1.00 FAL B:R26502 0.0 46.5 1.0 CAI B:R26502 1.3 47.1 1.0 FAJ B:R26502 2.1 47.6 1.0 FAK B:R26502 2.2 48.1 1.0 CAH B:R26502 2.3 45.9 1.0 CAM B:R26502 2.7 44.9 1.0 CAG B:R26502 3.6 45.0 1.0 CG1 B:VAL365 3.8 40.6 1.0 CB B:SER228 4.0 36.9 1.0 CAN B:R26502 4.1 45.5 1.0 N B:LYS134 4.1 30.7 1.0 CA B:LYS134 4.2 31.1 1.0 CD B:LYS367 4.4 31.4 1.0 C B:GLY133 4.4 30.2 1.0 OG B:SER228 4.5 37.4 1.0 CB B:LYS134 4.5 32.4 1.0 CAF B:R26502 4.7 44.7 1.0 O4 B:FAD501 4.7 31.6 1.0 CG B:LYS134 4.8 35.7 1.0 CB B:LYS367 4.8 29.9 1.0 O B:GLY133 4.8 29.4 1.0 NAO B:R26502 4.9 45.1 1.0 CAE B:R26502 4.9 46.1 1.0 CA B:GLY133 5.0 29.2 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:47.6 occ:1.00 FAJ B:R26502 0.0 47.6 1.0 CAI B:R26502 1.3 47.1 1.0 FAK B:R26502 2.1 48.1 1.0 FAL B:R26502 2.1 46.5 1.0 CAH B:R26502 2.3 45.9 1.0 CAG B:R26502 2.8 45.0 1.0 CAM B:R26502 3.5 44.9 1.0 ND2 B:ASN385 3.5 36.4 1.0 CB B:LYS367 3.6 29.9 1.0 CD B:LYS367 3.6 31.4 1.0 CG1 B:VAL365 3.8 40.6 1.0 CG B:LYS367 3.9 30.9 1.0 CAF B:R26502 4.1 44.7 1.0 CD2 B:HIS132 4.4 27.4 1.0 CAN B:R26502 4.6 45.5 1.0 NE2 B:HIS132 4.7 27.5 1.0 CG B:ASN385 4.8 34.9 1.0 O B:GLY133 4.8 29.4 1.0 C B:GLY133 4.9 30.2 1.0 CAE B:R26502 4.9 46.1 1.0 CE1 B:PHE369 4.9 28.6 1.0 CB B:VAL365 5.0 39.4 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN129


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 QN129 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:48.1 occ:1.00 FAK B:R26502 0.0 48.1 1.0 CAI B:R26502 1.3 47.1 1.0 FAJ B:R26502 2.1 47.6 1.0 FAL B:R26502 2.2 46.5 1.0 CAH B:R26502 2.3 45.9 1.0 CAG B:R26502 3.0 45.0 1.0 C B:GLY133 3.2 30.2 1.0 CAM B:R26502 3.3 44.9 1.0 CA B:GLY133 3.3 29.2 1.0 N B:LYS134 3.5 30.7 1.0 O B:GLY133 3.5 29.4 1.0 CD2 B:HIS132 3.7 27.4 1.0 O4 B:FAD501 3.8 31.6 1.0 N B:GLY133 4.0 28.4 1.0 CA B:LYS134 4.2 31.1 1.0 O B:HIS132 4.2 30.1 1.0 CD B:LYS367 4.2 31.4 1.0 CAF B:R26502 4.3 44.7 1.0 NE2 B:HIS132 4.3 27.5 1.0 C B:HIS132 4.3 28.5 1.0 CAN B:R26502 4.5 45.5 1.0 C4 B:FAD501 4.7 30.3 1.0 N3 B:FAD501 4.7 29.1 1.0 CG B:HIS132 4.8 27.8 1.0 CAE B:R26502 4.9 46.1 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