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Fluorine in PDB 6g83: Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)

Enzymatic activity of Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)

All present enzymatic activity of Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz):
1.1.98.3;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz), PDB code: 6g83 was solved by J.Piton, V.Makarov, S.T.Cole, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.164, 84.024, 81.666, 90.00, 103.98, 90.00
R / Rfree (%) 19.8 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz) (pdb code 6g83). 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 SPBTZ169 (Sulfonylpbtz), PDB code: 6g83:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6g83

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Fluorine binding site 1 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:56.2
occ:1.00
F16 A:EQ8502 0.0 56.2 1.0
C15 A:EQ8502 1.3 58.6 1.0
F18 A:EQ8502 2.1 56.5 1.0
F17 A:EQ8502 2.1 58.8 1.0
C13 A:EQ8502 2.4 58.0 1.0
H141 A:EQ8502 2.5 65.1 1.0
HB3 A:LYS367 2.8 55.9 1.0
C14 A:EQ8502 2.8 59.1 1.0
HD22 A:ASN385 2.8 48.0 1.0
HD3 A:LYS367 3.1 57.1 1.0
HD21 A:ASN385 3.1 48.0 1.0
ND2 A:ASN385 3.2 43.6 1.0
HE1 A:PHE369 3.2 45.7 1.0
HD2 A:LYS367 3.5 57.1 1.0
HD2 A:HIS132 3.5 50.0 1.0
CB A:LYS367 3.5 49.0 1.0
HB2 A:LYS367 3.5 55.9 1.0
CD A:LYS367 3.6 48.9 1.0
C12 A:EQ8502 3.7 57.4 1.0
HG12 A:VAL365 3.8 61.2 1.0
H121 A:EQ8502 3.9 61.7 1.0
CE1 A:PHE369 4.0 40.5 1.0
CG A:LYS367 4.1 47.3 1.0
CD2 A:HIS132 4.1 42.1 1.0
HZ A:PHE369 4.2 36.0 1.0
C04 A:EQ8502 4.2 58.9 1.0
CG A:ASN385 4.3 41.4 1.0
HG2 A:LYS367 4.3 52.7 1.0
NE2 A:HIS132 4.3 42.1 1.0
HB3 A:ASN385 4.4 34.4 1.0
HG11 A:VAL365 4.5 61.2 1.0
CZ A:PHE369 4.5 35.9 1.0
CG1 A:VAL365 4.6 52.1 1.0
HE22 A:GLN336 4.6 42.7 1.0
HE21 A:GLN336 4.8 42.7 1.0
CA A:LYS367 4.8 47.5 1.0
O A:GLY133 4.8 41.0 1.0
HA A:LYS134 4.8 49.9 1.0
C11 A:EQ8502 4.9 61.9 1.0
N A:LYS367 4.9 43.2 1.0
HB2 A:SER228 4.9 44.3 1.0
HG3 A:LYS367 4.9 52.7 1.0
NE2 A:GLN336 4.9 39.3 1.0
CB A:ASN385 4.9 37.3 1.0

Fluorine binding site 2 out of 6 in 6g83

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Fluorine binding site 2 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:58.8
occ:1.00
F17 A:EQ8502 0.0 58.8 1.0
C15 A:EQ8502 1.4 58.6 1.0
F16 A:EQ8502 2.1 56.2 1.0
F18 A:EQ8502 2.1 56.5 1.0
C13 A:EQ8502 2.4 58.0 1.0
H121 A:EQ8502 2.7 61.7 1.0
HD2 A:LYS367 2.8 57.1 1.0
C12 A:EQ8502 2.9 57.4 1.0
HG2 A:LYS134 3.1 75.9 1.0
HB2 A:LYS367 3.1 55.9 1.0
HB2 A:SER228 3.2 44.3 1.0
HB3 A:SER228 3.3 44.3 1.0
HA A:LYS134 3.4 49.9 1.0
HG12 A:VAL365 3.4 61.2 1.0
HB3 A:LYS367 3.4 55.9 1.0
HD3 A:LYS367 3.5 57.1 1.0
CD A:LYS367 3.5 48.9 1.0
C14 A:EQ8502 3.6 59.1 1.0
HG11 A:VAL365 3.7 61.2 1.0
CB A:LYS367 3.7 49.0 1.0
CB A:SER228 3.7 43.4 1.0
H141 A:EQ8502 3.8 65.1 1.0
CG1 A:VAL365 4.0 52.1 1.0
CG A:LYS134 4.0 57.8 1.0
HZ3 A:LYS134 4.1 78.5 1.0
CA A:LYS134 4.2 45.2 1.0
CG A:LYS367 4.2 47.3 1.0
HG3 A:LYS134 4.2 75.9 1.0
HZ2 A:LYS134 4.3 78.5 1.0
N A:LYS134 4.3 41.7 1.0
C11 A:EQ8502 4.3 61.9 1.0
HA A:SER228 4.3 48.7 1.0
HG13 A:VAL365 4.4 61.2 1.0
C A:GLY133 4.4 40.8 1.0
O A:GLY133 4.4 41.0 1.0
O A:SER227 4.6 45.1 1.0
NZ A:LYS134 4.6 60.0 1.0
HD2 A:HIS132 4.6 50.0 1.0
CB A:LYS134 4.6 50.0 1.0
CA A:SER228 4.7 45.9 1.0
H A:LYS134 4.7 43.4 1.0
HD22 A:ASN385 4.7 48.0 1.0
OG A:SER228 4.7 50.3 1.0
HE1 A:PHE369 4.7 45.7 1.0
HA2 A:GLY133 4.7 43.5 1.0
HG3 A:LYS367 4.8 52.7 1.0
HE2 A:LYS367 4.8 53.2 1.0
CE A:LYS367 4.8 47.2 1.0
C04 A:EQ8502 4.8 58.9 1.0
O A:PHE366 4.8 47.4 1.0
HG2 A:LYS367 4.9 52.7 1.0
HB3 A:LYS134 4.9 59.4 1.0
HG A:SER228 4.9 58.3 1.0
HZ3 A:LYS367 5.0 47.5 1.0

Fluorine binding site 3 out of 6 in 6g83

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Fluorine binding site 3 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:56.5
occ:1.00
F18 A:EQ8502 0.0 56.5 1.0
C15 A:EQ8502 1.3 58.6 1.0
F16 A:EQ8502 2.1 56.2 1.0
F17 A:EQ8502 2.1 58.8 1.0
C13 A:EQ8502 2.4 58.0 1.0
HD2 A:HIS132 2.6 50.0 1.0
HA2 A:GLY133 3.0 43.5 1.0
H121 A:EQ8502 3.1 61.7 1.0
C12 A:EQ8502 3.1 57.4 1.0
C A:GLY133 3.2 40.8 1.0
O A:GLY133 3.3 41.0 1.0
HD3 A:LYS367 3.4 57.1 1.0
C14 A:EQ8502 3.4 59.1 1.0
CD2 A:HIS132 3.5 42.1 1.0
HD2 A:LYS367 3.5 57.1 1.0
H141 A:EQ8502 3.5 65.1 1.0
CA A:GLY133 3.5 40.0 1.0
HA A:LYS134 3.7 49.9 1.0
N A:LYS134 3.7 41.7 1.0
HE1 A:PHE369 3.8 45.7 1.0
CD A:LYS367 3.9 48.9 1.0
N A:GLY133 4.1 37.9 1.0
H A:LYS134 4.1 43.4 1.0
NE2 A:HIS132 4.1 42.1 1.0
HG2 A:LYS134 4.1 75.9 1.0
O4 A:FAD501 4.2 45.6 1.0
CA A:LYS134 4.2 45.2 1.0
HN3 A:FAD501 4.4 38.0 1.0
HA3 A:GLY133 4.4 43.5 1.0
HB3 A:LYS367 4.4 55.9 1.0
C11 A:EQ8502 4.5 61.9 1.0
H A:GLY133 4.5 39.3 1.0
C A:HIS132 4.6 34.7 1.0
O A:HIS132 4.6 37.3 1.0
HG3 A:LYS134 4.6 75.9 1.0
CG A:HIS132 4.6 38.5 1.0
C04 A:EQ8502 4.7 58.9 1.0
HE2 A:LYS367 4.7 53.2 1.0
CE1 A:PHE369 4.7 40.5 1.0
HB2 A:LYS367 4.7 55.9 1.0
CG A:LYS134 4.8 57.8 1.0
HB2 A:HIS132 4.8 41.3 1.0
HZ A:PHE369 4.9 36.0 1.0
CB A:LYS367 4.9 49.0 1.0
HD21 A:ASN385 4.9 48.0 1.0
HD22 A:ASN385 4.9 48.0 1.0
CE A:LYS367 4.9 47.2 1.0
HH A:TYR314 4.9 76.6 1.0
CG A:LYS367 5.0 47.3 1.0

Fluorine binding site 4 out of 6 in 6g83

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Fluorine binding site 4 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:67.5
occ:1.00
F16 B:EQ8502 0.0 67.5 1.0
C15 B:EQ8502 1.3 64.3 1.0
F18 B:EQ8502 2.1 70.7 1.0
F17 B:EQ8502 2.1 71.0 1.0
C13 B:EQ8502 2.4 66.8 1.0
H121 B:EQ8502 2.7 79.1 1.0
HD2 B:HIS132 2.8 49.1 1.0
HA2 B:GLY133 2.9 49.7 1.0
C12 B:EQ8502 2.9 69.6 1.0
C B:GLY133 2.9 46.7 1.0
O B:GLY133 3.0 43.9 1.0
HA B:LYS134 3.2 56.9 1.0
N B:LYS134 3.3 48.0 1.0
CA B:GLY133 3.3 45.7 1.0
C14 B:EQ8502 3.5 68.1 1.0
H B:LYS134 3.7 49.8 1.0
CD2 B:HIS132 3.7 45.4 1.0
H141 B:EQ8502 3.7 74.5 1.0
HG2 B:LYS367 3.8 58.0 1.0
CA B:LYS134 3.8 51.6 1.0
HE1 B:PHE369 3.8 51.5 1.0
N B:GLY133 4.0 43.5 1.0
HG2 B:LYS134 4.0 70.4 1.0
HZ2 B:LYS367 4.2 71.3 1.0
HA3 B:GLY133 4.2 49.7 1.0
C11 B:EQ8502 4.2 69.0 1.0
HB2 B:LYS367 4.3 66.5 1.0
H B:GLY133 4.3 45.1 1.0
NE2 B:HIS132 4.4 47.0 1.0
HG3 B:LYS134 4.5 70.4 1.0
HB3 B:LYS367 4.5 66.5 1.0
C B:HIS132 4.5 42.7 1.0
O4 B:FAD501 4.5 51.8 1.0
CG B:LYS367 4.6 54.1 1.0
CG B:LYS134 4.6 58.4 1.0
O B:HIS132 4.6 40.6 1.0
CB B:LYS367 4.7 58.5 1.0
C04 B:EQ8502 4.7 67.9 1.0
HN3 B:FAD501 4.7 48.5 1.0
CE1 B:PHE369 4.7 48.2 1.0
CB B:LYS134 4.8 54.5 1.0
CG B:HIS132 4.8 43.3 1.0
HD3 B:LYS367 4.8 75.4 1.0
HB3 B:SER228 4.9 42.0 1.0
C B:LYS134 4.9 50.4 1.0
HB2 B:HIS132 4.9 41.8 1.0
HB2 B:HIS136 4.9 50.8 1.0
NZ B:LYS367 5.0 59.8 1.0
C05 B:EQ8502 5.0 75.5 1.0
HG11 B:VAL365 5.0 72.8 1.0

Fluorine binding site 5 out of 6 in 6g83

Go back to Fluorine Binding Sites List in 6g83
Fluorine binding site 5 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:71.0
occ:1.00
F17 B:EQ8502 0.0 71.0 1.0
C15 B:EQ8502 1.3 64.3 1.0
F16 B:EQ8502 2.1 67.5 1.0
F18 B:EQ8502 2.2 70.7 1.0
C13 B:EQ8502 2.4 66.8 1.0
H141 B:EQ8502 2.5 74.5 1.0
C14 B:EQ8502 2.8 68.1 1.0
HB3 B:LYS367 3.0 66.5 1.0
HE1 B:PHE369 3.0 51.5 1.0
HD2 B:HIS132 3.1 49.1 1.0
HD22 B:ASN385 3.1 60.7 1.0
HD21 B:ASN385 3.2 60.7 1.0
HG2 B:LYS367 3.3 58.0 1.0
ND2 B:ASN385 3.3 54.1 1.0
HB2 B:LYS367 3.3 66.5 1.0
CB B:LYS367 3.5 58.5 1.0
CD2 B:HIS132 3.6 45.4 1.0
C12 B:EQ8502 3.7 69.6 1.0
HZ B:PHE369 3.7 45.0 1.0
CE1 B:PHE369 3.7 48.2 1.0
NE2 B:HIS132 3.9 47.0 1.0
CG B:LYS367 3.9 54.1 1.0
H121 B:EQ8502 3.9 79.1 1.0
CZ B:PHE369 4.0 45.5 1.0
CG B:ASN385 4.2 51.5 1.0
C04 B:EQ8502 4.3 67.9 1.0
HG12 B:VAL365 4.3 72.8 1.0
HG3 B:LYS367 4.4 58.0 1.0
HB3 B:ASN385 4.4 45.1 1.0
HE22 B:GLN336 4.5 46.4 1.0
O B:GLY133 4.5 43.9 1.0
HZ2 B:LYS367 4.7 71.3 1.0
HA B:LYS134 4.7 56.9 1.0
HG11 B:VAL365 4.7 72.8 1.0
HE21 B:GLN336 4.7 46.4 1.0
CD1 B:PHE369 4.8 51.0 1.0
HA2 B:GLY133 4.8 49.7 1.0
C B:GLY133 4.8 46.7 1.0
CG B:HIS132 4.9 43.3 1.0
HD3 B:LYS367 4.9 75.4 1.0
C11 B:EQ8502 4.9 69.0 1.0
NE2 B:GLN336 4.9 47.6 1.0
CA B:LYS367 4.9 57.0 1.0
HD1 B:PHE369 4.9 57.5 1.0
OD1 B:ASN385 4.9 49.1 1.0
CB B:ASN385 4.9 46.5 1.0
CG1 B:VAL365 5.0 63.7 1.0

Fluorine binding site 6 out of 6 in 6g83

Go back to Fluorine Binding Sites List in 6g83
Fluorine binding site 6 out of 6 in the Crystal Structure of M. Tuberculosis DPRE1 in Complex with SPBTZ169 (Sulfonylpbtz)


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 SPBTZ169 (Sulfonylpbtz) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:70.7
occ:1.00
F18 B:EQ8502 0.0 70.7 1.0
C15 B:EQ8502 1.3 64.3 1.0
F16 B:EQ8502 2.1 67.5 1.0
F17 B:EQ8502 2.2 71.0 1.0
C13 B:EQ8502 2.4 66.8 1.0
HB2 B:LYS367 2.5 66.5 1.0
H121 B:EQ8502 2.8 79.1 1.0
C12 B:EQ8502 3.0 69.6 1.0
HG2 B:LYS367 3.1 58.0 1.0
CB B:LYS367 3.2 58.5 1.0
HB3 B:LYS367 3.3 66.5 1.0
HA B:LYS134 3.3 56.9 1.0
HB3 B:SER228 3.4 42.0 1.0
HG12 B:VAL365 3.4 72.8 1.0
HB2 B:SER228 3.5 42.0 1.0
C14 B:EQ8502 3.5 68.1 1.0
HG11 B:VAL365 3.5 72.8 1.0
HD3 B:LYS367 3.6 75.4 1.0
CG B:LYS367 3.6 54.1 1.0
HG2 B:LYS134 3.7 70.4 1.0
H141 B:EQ8502 3.7 74.5 1.0
CB B:SER228 3.9 45.3 1.0
CG1 B:VAL365 3.9 63.7 1.0
CD B:LYS367 4.1 62.4 1.0
CA B:LYS134 4.2 51.6 1.0
HZ2 B:LYS367 4.2 71.3 1.0
HG13 B:VAL365 4.3 72.8 1.0
C11 B:EQ8502 4.3 69.0 1.0
HD22 B:ASN385 4.4 60.7 1.0
O B:GLY133 4.4 43.9 1.0
N B:LYS134 4.4 48.0 1.0
HA B:SER228 4.4 50.2 1.0
HG3 B:LYS367 4.5 58.0 1.0
C B:GLY133 4.5 46.7 1.0
CA B:LYS367 4.5 57.0 1.0
CG B:LYS134 4.5 58.4 1.0
O B:SER227 4.5 47.1 1.0
HE1 B:PHE369 4.6 51.5 1.0
HD2 B:HIS132 4.6 49.1 1.0
HZ3 B:LYS134 4.6 0.8 1.0
C04 B:EQ8502 4.7 67.9 1.0
O B:PHE366 4.7 57.3 1.0
HA B:LYS367 4.7 62.2 1.0
HD21 B:ASN385 4.8 60.7 1.0
HD2 B:LYS367 4.8 75.4 1.0
CA B:SER228 4.8 49.5 1.0
HG3 B:LYS134 4.8 70.4 1.0
H B:LYS134 4.8 49.8 1.0
ND2 B:ASN385 4.8 54.1 1.0
CB B:LYS134 4.9 54.5 1.0
HA2 B:GLY133 4.9 49.7 1.0
N B:LYS367 4.9 57.2 1.0
NZ B:LYS367 4.9 59.8 1.0
OG B:SER228 4.9 58.4 1.0
HZ2 B:LYS134 4.9 0.8 1.0
C B:PHE366 4.9 58.5 1.0
HZ3 B:LYS367 5.0 71.3 1.0
C05 B:EQ8502 5.0 75.5 1.0

Reference:

J.Piton, A.Vocat, A.Lupien, C.S.Foo, O.Riabova, V.Makarov, S.T.Cole. Structure-Based Drug Design and Characterization of Sulfonyl-Piperazine Benzothiazinone Inhibitors of DPRE1 From Mycobacterium Tuberculosis. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30012754
DOI: 10.1128/AAC.00681-18
Page generated: Tue Jul 15 11:46:42 2025

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