Fluorine in PDB 4p8n: Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118

The structure of Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118, PDB code: 4p8n 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)	41.60 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.242, 83.219, 80.755, 90.00, 103.04, 90.00
R / Rfree (%)	20.3 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118 (pdb code 4p8n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118, PDB code: 4p8n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:33.7 occ:0.50 FAU A:R57502 0.0 33.7 0.5 CAU A:R57502 1.3 32.8 0.5 CAV A:R57502 2.4 32.8 0.5 CAT A:R57502 2.4 32.2 0.5 OAW A:R57502 2.7 33.4 0.5 NE A:ARG325 3.1 65.0 1.0 CZ A:ARG325 3.4 64.0 1.0 CD A:ARG325 3.5 64.2 1.0 CG A:ARG325 3.6 64.8 1.0 CAY A:R57502 3.6 32.3 0.5 CAS A:R57502 3.6 31.7 0.5 CD1 A:LEU363 3.7 41.6 1.0 NH2 A:ARG325 3.8 61.8 1.0 CB A:ASN324 3.9 63.5 1.0 CD1 A:LEU317 4.0 48.9 1.0 CG A:ASN324 4.0 64.5 1.0 NH1 A:ARG325 4.0 64.4 1.0 CAX A:R57502 4.1 33.6 0.5 CAZ A:R57502 4.1 32.1 0.5 OD1 A:ASN324 4.2 65.3 1.0 ND2 A:ASN324 4.5 63.9 1.0 CAT A:R57502 4.9 37.3 0.5 CAR A:R57502 4.9 30.5 0.5

Fluorine binding site 2 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:39.2 occ:0.50 FAU A:R57502 0.0 39.2 0.5 CAU A:R57502 1.3 38.3 0.5 CAV A:R57502 2.4 38.5 0.5 CAT A:R57502 2.4 37.3 0.5 CAX A:R57502 2.5 39.3 0.5 OAW A:R57502 2.8 39.1 0.5 CG1 A:VAL365 3.4 32.5 1.0 CAY A:R57502 3.6 38.0 0.5 CAS A:R57502 3.6 36.3 0.5 CB A:LEU363 3.7 36.9 1.0 CD1 A:LEU317 3.9 48.9 1.0 N A:ASN364 3.9 31.0 1.0 C A:LEU363 3.9 33.8 1.0 CA A:LEU363 4.1 35.1 1.0 CAZ A:R57502 4.1 37.1 0.5 C A:ASN364 4.4 30.4 1.0 N A:VAL365 4.4 28.5 1.0 O A:LEU363 4.4 35.2 1.0 O A:HOH766 4.4 40.4 1.0 CAR A:R57502 4.5 30.5 0.5 CAT A:R57502 4.5 32.2 0.5 CG A:LEU363 4.6 39.8 1.0 CB A:VAL365 4.6 31.5 1.0 CD2 A:LEU363 4.6 40.7 1.0 CA A:ASN364 4.6 29.7 1.0 O A:ASN364 4.7 30.4 1.0 CG A:LEU317 4.7 48.5 1.0 CD1 A:LEU363 4.8 41.6 1.0 CAS A:R57502 4.8 31.7 0.5 CA A:VAL365 4.9 28.9 1.0 CD1 A:TRP230 4.9 31.1 0.5 CAR A:R57502 4.9 34.0 0.5 NAQ A:R57502 4.9 29.2 0.5 NAQ A:R57502 4.9 31.9 0.5 CD1 A:TRP230 4.9 27.8 0.5

Fluorine binding site 3 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:29.1 occ:0.50 FAJ A:R57502 0.0 29.1 0.5 FAJ A:R57502 0.5 30.5 0.5 CAI A:R57502 1.2 30.4 0.5 CAI A:R57502 1.3 28.7 0.5 FAK A:R57502 1.8 30.8 0.5 FAL A:R57502 2.1 29.0 0.5 FAK A:R57502 2.2 28.9 0.5 CAH A:R57502 2.2 29.8 0.5 FAL A:R57502 2.3 31.0 0.5 CAH A:R57502 2.3 28.1 0.5 CAG A:R57502 2.9 29.2 0.5 CAG A:R57502 3.1 27.6 0.5 CAM A:R57502 3.2 29.7 0.5 C A:GLY133 3.2 19.0 1.0 CAM A:R57502 3.3 28.1 0.5 O A:GLY133 3.5 18.8 1.0 CA A:GLY133 3.5 19.5 1.0 N A:LYS134 3.6 19.4 1.0 CD2 A:HIS132 3.8 17.5 1.0 O4 A:FAD501 3.8 21.0 1.0 CA A:LYS134 4.1 20.2 1.0 CAF A:R57502 4.2 29.1 0.5 N A:GLY133 4.2 18.2 1.0 CD A:LYS367 4.2 24.4 1.0 O A:HIS132 4.3 17.2 1.0 CAF A:R57502 4.3 27.6 0.5 CAN A:R57502 4.4 29.1 0.5 CAN A:R57502 4.5 27.6 0.5 C A:HIS132 4.5 17.6 1.0 NE2 A:HIS132 4.5 18.7 1.0 C4 A:FAD501 4.7 20.4 1.0 CAE A:R57502 4.8 29.3 0.5 N3 A:FAD501 4.8 19.9 1.0 CAE A:R57502 4.9 27.7 0.5 CG A:HIS132 4.9 17.6 1.0 CB A:LYS134 5.0 21.5 1.0

Fluorine binding site 4 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:30.5 occ:0.50 FAJ A:R57502 0.0 30.5 0.5 FAJ A:R57502 0.5 29.1 0.5 CAI A:R57502 1.3 30.4 0.5 CAI A:R57502 1.3 28.7 0.5 FAL A:R57502 1.9 29.0 0.5 FAL A:R57502 2.1 31.0 0.5 FAK A:R57502 2.2 30.8 0.5 CAH A:R57502 2.3 29.8 0.5 FAK A:R57502 2.3 28.9 0.5 CAH A:R57502 2.4 28.1 0.5 CAG A:R57502 2.8 29.2 0.5 CAG A:R57502 3.0 27.6 0.5 C A:GLY133 3.3 19.0 1.0 O A:GLY133 3.4 18.8 1.0 CAM A:R57502 3.5 29.7 0.5 CD2 A:HIS132 3.5 17.5 1.0 CAM A:R57502 3.5 28.1 0.5 CA A:GLY133 3.6 19.5 1.0 N A:LYS134 3.8 19.4 1.0 CD A:LYS367 4.0 24.4 1.0 O4 A:FAD501 4.1 21.0 1.0 N A:GLY133 4.2 18.2 1.0 CAF A:R57502 4.2 29.1 0.5 NE2 A:HIS132 4.2 18.7 1.0 CA A:LYS134 4.3 20.2 1.0 CAF A:R57502 4.3 27.6 0.5 O A:HIS132 4.3 17.2 1.0 C A:HIS132 4.4 17.6 1.0 CAN A:R57502 4.6 29.1 0.5 CG A:HIS132 4.6 17.6 1.0 CAN A:R57502 4.7 27.6 0.5 CG A:LYS367 4.7 24.3 1.0 CB A:LYS367 4.8 23.4 1.0 N3 A:FAD501 4.8 19.9 1.0 CE1 A:PHE369 4.9 19.9 1.0 C4 A:FAD501 4.9 20.4 1.0 CAE A:R57502 4.9 29.3 0.5 CAE A:R57502 5.0 27.7 0.5

Fluorine binding site 5 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:28.9 occ:0.50 FAK A:R57502 0.0 28.9 0.5 FAK A:R57502 0.9 30.8 0.5 CAI A:R57502 1.2 30.4 0.5 CAI A:R57502 1.3 28.7 0.5 FAL A:R57502 1.4 31.0 0.5 FAL A:R57502 2.2 29.0 0.5 FAJ A:R57502 2.2 29.1 0.5 CAH A:R57502 2.2 29.8 0.5 CAH A:R57502 2.3 28.1 0.5 FAJ A:R57502 2.3 30.5 0.5 CAM A:R57502 2.7 29.7 0.5 CAM A:R57502 2.7 28.1 0.5 CAG A:R57502 3.4 29.2 0.5 CAG A:R57502 3.6 27.6 0.5 CB A:SER228 3.8 20.8 1.0 CAN A:R57502 4.1 29.1 0.5 CG2 A:VAL365 4.1 32.8 1.0 CAN A:R57502 4.1 27.6 0.5 CB A:LYS367 4.3 23.4 1.0 CD A:LYS367 4.3 24.4 1.0 OG A:SER228 4.5 22.3 1.0 CA A:LYS134 4.5 20.2 1.0 CAF A:R57502 4.6 29.1 0.5 N A:LYS134 4.6 19.4 1.0 O A:HOH788 4.6 38.3 1.0 CAF A:R57502 4.7 27.6 0.5 CB A:VAL365 4.7 31.5 1.0 C A:GLY133 4.8 19.0 1.0 CAE A:R57502 4.8 29.3 0.5 CG A:LYS367 4.9 24.3 1.0 CAE A:R57502 4.9 27.7 0.5 NAO A:R57502 4.9 29.5 0.5 CB A:LYS134 5.0 21.5 1.0 O A:GLY133 5.0 18.8 1.0

Fluorine binding site 6 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:30.8 occ:0.50 FAK A:R57502 0.0 30.8 0.5 FAK A:R57502 0.9 28.9 0.5 CAI A:R57502 1.3 30.4 0.5 CAI A:R57502 1.6 28.7 0.5 FAJ A:R57502 1.8 29.1 0.5 FAL A:R57502 2.2 31.0 0.5 FAJ A:R57502 2.2 30.5 0.5 CAH A:R57502 2.3 29.8 0.5 CAH A:R57502 2.5 28.1 0.5 CAM A:R57502 2.7 29.7 0.5 FAL A:R57502 2.7 29.0 0.5 CAM A:R57502 2.7 28.1 0.5 CAG A:R57502 3.6 29.2 0.5 CAG A:R57502 3.8 27.6 0.5 N A:LYS134 3.9 19.4 1.0 CA A:LYS134 4.0 20.2 1.0 CAN A:R57502 4.0 29.1 0.5 CB A:SER228 4.0 20.8 1.0 CAN A:R57502 4.1 27.6 0.5 C A:GLY133 4.2 19.0 1.0 O A:HOH788 4.3 38.3 1.0 CB A:LYS134 4.3 21.5 1.0 O4 A:FAD501 4.5 21.0 1.0 OG A:SER228 4.5 22.3 1.0 O A:GLY133 4.6 18.8 1.0 CD A:LYS367 4.6 24.4 1.0 CAF A:R57502 4.7 29.1 0.5 CA A:GLY133 4.7 19.5 1.0 CG A:LYS134 4.7 24.4 1.0 CAF A:R57502 4.9 27.6 0.5 NAO A:R57502 4.9 29.5 0.5 CAE A:R57502 4.9 29.3 0.5 CG2 A:VAL365 4.9 32.8 1.0 NAO A:R57502 4.9 27.9 0.5 CAE A:R57502 5.0 27.7 0.5

Fluorine binding site 7 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:29.0 occ:0.50 FAL A:R57502 0.0 29.0 0.5 FAL A:R57502 0.9 31.0 0.5 CAI A:R57502 1.3 28.7 0.5 CAI A:R57502 1.5 30.4 0.5 FAJ A:R57502 1.9 30.5 0.5 FAJ A:R57502 2.1 29.1 0.5 FAK A:R57502 2.2 28.9 0.5 CAH A:R57502 2.3 28.1 0.5 CAH A:R57502 2.3 29.8 0.5 CAG A:R57502 2.6 29.2 0.5 CAG A:R57502 2.7 27.6 0.5 FAK A:R57502 2.7 30.8 0.5 ND2 A:ASN385 3.5 22.4 1.0 CAM A:R57502 3.5 28.1 0.5 CAM A:R57502 3.5 29.7 0.5 CB A:LYS367 3.6 23.4 1.0 CD A:LYS367 3.8 24.4 1.0 CAF A:R57502 3.9 29.1 0.5 CG A:LYS367 4.0 24.3 1.0 CG2 A:VAL365 4.0 32.8 1.0 CD2 A:HIS132 4.0 17.5 1.0 CAF A:R57502 4.0 27.6 0.5 NE2 A:HIS132 4.3 18.7 1.0 CE1 A:PHE369 4.5 19.9 1.0 CAN A:R57502 4.6 29.1 0.5 CAN A:R57502 4.6 27.6 0.5 CG A:ASN385 4.6 20.6 1.0 O A:GLY133 4.7 18.8 1.0 CAE A:R57502 4.7 29.3 0.5 CAE A:R57502 4.8 27.7 0.5 CA A:LYS367 4.9 20.9 1.0 C A:GLY133 4.9 19.0 1.0

Fluorine binding site 8 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


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 QN118 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:31.0 occ:0.50 FAL A:R57502 0.0 31.0 0.5 FAL A:R57502 0.9 29.0 0.5 CAI A:R57502 1.2 28.7 0.5 CAI A:R57502 1.3 30.4 0.5 FAK A:R57502 1.4 28.9 0.5 FAJ A:R57502 2.1 30.5 0.5 FAK A:R57502 2.2 30.8 0.5 FAJ A:R57502 2.3 29.1 0.5 CAH A:R57502 2.3 29.8 0.5 CAH A:R57502 2.3 28.1 0.5 CAG A:R57502 3.0 29.2 0.5 CAG A:R57502 3.1 27.6 0.5 CAM A:R57502 3.3 28.1 0.5 CAM A:R57502 3.3 29.7 0.5 CB A:LYS367 3.4 23.4 1.0 CG2 A:VAL365 3.7 32.8 1.0 CD A:LYS367 3.8 24.4 1.0 CG A:LYS367 4.0 24.3 1.0 ND2 A:ASN385 4.1 22.4 1.0 CAF A:R57502 4.3 29.1 0.5 CAF A:R57502 4.4 27.6 0.5 CAN A:R57502 4.5 29.1 0.5 CB A:SER228 4.5 20.8 1.0 CAN A:R57502 4.5 27.6 0.5 CB A:VAL365 4.7 31.5 1.0 CA A:LYS367 4.7 20.9 1.0 O A:PHE366 4.8 20.4 1.0 CAE A:R57502 4.9 29.3 0.5 N A:LYS367 4.9 20.7 1.0 CD2 A:HIS132 4.9 17.5 1.0 O A:GLY133 4.9 18.8 1.0 CAE A:R57502 4.9 27.7 0.5 C A:PHE366 4.9 21.6 1.0

Fluorine binding site 9 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:43.7 occ:0.50 FAU B:R57502 0.0 43.7 0.5 CAU B:R57502 1.3 43.8 0.5 CAT B:R57502 2.4 43.4 0.5 CAV B:R57502 2.4 44.0 0.5 OAW B:R57502 2.8 44.2 0.5 O B:PRO316 3.6 61.5 1.0 CAY B:R57502 3.6 43.6 0.5 CAS B:R57502 3.6 43.0 1.0 CAX B:R57502 3.7 44.2 0.5 CD B:PRO316 4.0 57.8 1.0 CAZ B:R57502 4.1 43.2 0.5 CG B:PRO316 4.2 58.9 1.0 C B:PRO316 4.8 59.6 1.0 N B:PRO316 4.8 57.3 1.0 CAR B:R57502 4.9 41.4 1.0

Fluorine binding site 10 out of 12 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of M. Tuberculosis DPRE1 in Complex with the Non- Covalent Inhibitor QN118 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:38.2 occ:1.00 FAJ B:R57502 0.0 38.2 1.0 CAI B:R57502 1.3 37.0 1.0 FAK B:R57502 2.2 38.6 1.0 FAL B:R57502 2.2 38.0 1.0 CAH B:R57502 2.3 35.7 1.0 CAG B:R57502 2.9 33.8 1.0 C B:GLY133 3.2 22.2 1.0 O B:GLY133 3.3 21.4 1.0 CAM B:R57502 3.4 34.7 1.0 CA B:GLY133 3.4 22.5 1.0 CD2 B:HIS132 3.5 21.3 1.0 N B:LYS134 3.6 22.1 1.0 O4 B:FAD501 3.9 25.0 1.0 N B:GLY133 4.0 21.4 1.0 CD B:LYS367 4.1 29.5 1.0 CAF B:R57502 4.2 33.7 1.0 CA B:LYS134 4.2 22.8 1.0 NE2 B:HIS132 4.2 21.9 1.0 O B:HIS132 4.3 21.7 1.0 C B:HIS132 4.3 20.9 1.0 CAN B:R57502 4.5 35.2 1.0 CG B:HIS132 4.6 20.9 1.0 C4 B:FAD501 4.7 25.3 1.0 N3 B:FAD501 4.7 24.5 1.0 CAE B:R57502 4.9 34.9 1.0 CG B:LYS367 5.0 29.1 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