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Fluorine in PDB 4bqp: Mtb Inha Complex with Methyl-Thiazole Compound 7

Enzymatic activity of Mtb Inha Complex with Methyl-Thiazole Compound 7

All present enzymatic activity of Mtb Inha Complex with Methyl-Thiazole Compound 7:
1.3.1.9;

Protein crystallography data

The structure of Mtb Inha Complex with Methyl-Thiazole Compound 7, PDB code: 4bqp was solved by J.A.Read, H.Gingell, P.Madhavapeddi, P.S.Shirude, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.05 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.297, 81.304, 189.004, 90.00, 95.25, 90.00
R / Rfree (%) 20.8 / 23.34

Other elements in 4bqp:

The structure of Mtb Inha Complex with Methyl-Thiazole Compound 7 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Mtb Inha Complex with Methyl-Thiazole Compound 7 (pdb code 4bqp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Mtb Inha Complex with Methyl-Thiazole Compound 7, PDB code: 4bqp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4bqp

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Fluorine binding site 1 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1272

b:7.7
occ:1.00
 F1 A:VMY1272 0.0 7.7 1.0
C13 A:VMY1272 1.4 9.4 1.0
C14 A:VMY1272 2.3 12.1 1.0
C12 A:VMY1272 2.3 4.0 1.0
C11 A:VMY1272 2.8 4.0 1.0
C A:ALA198 3.3 14.1 1.0
O A:ALA198 3.3 14.9 1.0
CB A:ALA198 3.4 13.1 1.0
N A:MET199 3.5 10.1 1.0
C17 A:VMY1272 3.6 9.8 1.0
C15 A:VMY1272 3.6 12.8 1.0
N5 A:VMY1272 3.6 6.3 1.0
N4 A:VMY1272 3.7 5.7 1.0
S A:VMY1272 3.7 7.0 1.0
SD A:MET199 3.8 20.9 1.0
CA A:MET199 3.8 9.6 1.0
CG2 A:ILE202 3.9 6.7 1.0
CA A:ALA198 4.0 12.7 1.0
S1 A:VMY1272 4.0 5.8 1.0
CG A:MET199 4.0 15.9 1.0
C16 A:VMY1272 4.1 12.6 1.0
CE A:MET103 4.2 6.3 1.0
CB A:MET199 4.6 10.9 1.0
F A:VMY1272 4.7 13.6 1.0
C2 A:VMY1272 4.7 6.3 1.0
CB A:ILE202 4.8 7.9 1.0
C8 A:VMY1272 5.0 6.3 1.0

Fluorine binding site 2 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 2 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1272

b:13.6
occ:1.00
 F A:VMY1272 0.0 13.6 1.0
C17 A:VMY1272 1.3 9.8 1.0
C16 A:VMY1272 2.3 12.6 1.0
C12 A:VMY1272 2.3 4.0 1.0
C11 A:VMY1272 2.8 4.0 1.0
CA A:GLY104 3.1 4.3 1.0
N4 A:VMY1272 3.2 5.7 1.0
C10 A:VMY1272 3.3 6.9 1.0
CD1 A:ILE202 3.3 7.0 1.0
N A:GLY104 3.4 3.0 1.0
C13 A:VMY1272 3.6 9.4 1.0
C15 A:VMY1272 3.6 12.8 1.0
CD2 A:LEU207 3.6 15.0 1.0
C A:MET103 3.8 6.1 1.0
O A:MET103 4.0 9.1 1.0
C14 A:VMY1272 4.1 12.1 1.0
CG A:MET103 4.2 6.7 1.0
N5 A:VMY1272 4.2 6.3 1.0
C A:GLY104 4.3 8.3 1.0
C9 A:VMY1272 4.3 9.3 1.0
O A:ALA157 4.3 3.7 1.0
CB A:ALA157 4.4 5.3 1.0
CE A:MET103 4.6 6.3 1.0
CG1 A:ILE202 4.6 7.3 1.0
F1 A:VMY1272 4.7 7.7 1.0
CB A:MET103 4.7 3.4 1.0
O A:GLY104 4.8 10.2 1.0
CA A:MET103 4.8 4.2 1.0
CB A:ILE202 4.8 7.9 1.0
C8 A:VMY1272 4.8 6.3 1.0
C A:ALA157 4.9 3.7 1.0
SD A:MET103 4.9 7.2 1.0

Fluorine binding site 3 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 3 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1271

b:7.5
occ:1.00
 F1 B:VMY1271 0.0 7.5 1.0
C13 B:VMY1271 1.4 10.9 1.0
C14 B:VMY1271 2.3 10.8 1.0
C12 B:VMY1271 2.4 8.2 1.0
C11 B:VMY1271 2.9 4.4 1.0
C B:ALA198 3.4 11.2 1.0
O B:ALA198 3.5 10.9 1.0
CB B:ALA198 3.5 9.8 1.0
N B:MET199 3.6 9.0 1.0
C17 B:VMY1271 3.6 13.4 1.0
C15 B:VMY1271 3.6 13.2 1.0
SD B:MET199 3.6 19.1 1.0
N5 B:VMY1271 3.6 5.8 1.0
S B:VMY1271 3.7 9.5 1.0
N4 B:VMY1271 3.7 7.7 1.0
CA B:MET199 3.8 10.2 1.0
CG2 B:ILE202 3.8 8.4 1.0
CG B:MET199 3.9 14.2 1.0
S1 B:VMY1271 4.0 6.2 1.0
C16 B:VMY1271 4.1 13.5 1.0
CA B:ALA198 4.1 9.4 1.0
CE B:MET103 4.3 7.3 1.0
CB B:MET199 4.5 11.7 1.0
C2 B:VMY1271 4.6 7.8 1.0
F B:VMY1271 4.7 18.0 1.0
CB B:ILE202 4.8 8.8 1.0
C8 B:VMY1271 5.0 4.0 1.0

Fluorine binding site 4 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 4 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1271

b:18.0
occ:1.00
 F B:VMY1271 0.0 18.0 1.0
C17 B:VMY1271 1.3 13.4 1.0
C12 B:VMY1271 2.3 8.2 1.0
C16 B:VMY1271 2.3 13.5 1.0
C11 B:VMY1271 2.8 4.4 1.0
CA B:GLY104 3.0 7.3 1.0
N4 B:VMY1271 3.2 7.7 1.0
C10 B:VMY1271 3.3 6.4 1.0
CD1 B:ILE202 3.3 4.2 1.0
N B:GLY104 3.3 5.5 1.0
CD2 B:LEU207 3.4 12.8 1.0
C13 B:VMY1271 3.6 10.9 1.0
C15 B:VMY1271 3.6 13.2 1.0
C B:MET103 3.8 6.5 1.0
O B:MET103 3.9 8.0 1.0
C14 B:VMY1271 4.1 10.8 1.0
N5 B:VMY1271 4.1 5.8 1.0
CG B:MET103 4.2 8.4 1.0
C B:GLY104 4.3 11.5 1.0
C9 B:VMY1271 4.3 5.8 1.0
CB B:ALA157 4.4 6.0 1.0
CG1 B:ILE202 4.6 7.8 1.0
O B:ALA157 4.6 5.6 1.0
CE B:MET103 4.7 7.3 1.0
F1 B:VMY1271 4.7 7.5 1.0
C8 B:VMY1271 4.7 4.0 1.0
CB B:ILE202 4.7 8.8 1.0
O B:GLY104 4.8 10.2 1.0
CA B:MET103 4.8 7.2 1.0
CB B:MET103 4.8 5.2 1.0
CG B:LEU207 4.9 9.6 1.0
SD B:MET103 4.9 9.2 1.0

Fluorine binding site 5 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 5 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1271

b:39.4
occ:1.00
 F1 C:VMY1271 0.0 39.4 1.0
C13 C:VMY1271 1.4 40.2 1.0
C14 C:VMY1271 2.3 40.8 1.0
C12 C:VMY1271 2.3 38.2 1.0
C11 C:VMY1271 2.8 34.2 1.0
N5 C:VMY1271 3.3 29.0 1.0
O C:ALA198 3.4 27.0 1.0
N4 C:VMY1271 3.5 29.1 1.0
C C:ALA198 3.6 27.3 1.0
C17 C:VMY1271 3.6 41.7 1.0
C15 C:VMY1271 3.6 40.9 1.0
S1 C:VMY1271 3.6 24.5 1.0
S C:VMY1271 3.7 25.6 1.0
CB C:ALA198 3.7 22.8 1.0
N C:MET199 3.9 25.4 1.0
C16 C:VMY1271 4.1 41.2 1.0
CA C:MET199 4.2 26.4 1.0
CA C:ALA198 4.3 22.0 1.0
SD C:MET199 4.4 38.4 1.0
CB C:ILE202 4.4 30.4 1.0
CE C:MET103 4.5 26.5 1.0
C8 C:VMY1271 4.7 28.3 1.0
F C:VMY1271 4.7 44.8 1.0
C2 C:VMY1271 4.8 25.3 1.0
C10 C:VMY1271 4.9 29.0 1.0
O C:VMY1271 4.9 24.1 1.0
C3 C:VMY1271 5.0 25.7 1.0
CB C:MET199 5.0 29.4 1.0

Fluorine binding site 6 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 6 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1271

b:44.8
occ:1.00
 F C:VMY1271 0.0 44.8 1.0
C17 C:VMY1271 1.4 41.7 1.0
C12 C:VMY1271 2.3 38.2 1.0
C16 C:VMY1271 2.3 41.2 1.0
C11 C:VMY1271 2.8 34.2 1.0
CA C:GLY104 3.0 27.8 1.0
N C:GLY104 3.1 27.7 1.0
N4 C:VMY1271 3.3 29.1 1.0
C10 C:VMY1271 3.5 29.0 1.0
C13 C:VMY1271 3.6 40.2 1.0
C15 C:VMY1271 3.6 40.9 1.0
C C:MET103 4.1 31.1 1.0
C14 C:VMY1271 4.1 40.8 1.0
CB C:MET103 4.2 23.5 1.0
CB C:ILE202 4.3 30.4 1.0
CB C:LEU207 4.3 48.5 1.0
N5 C:VMY1271 4.4 29.0 1.0
C C:GLY104 4.4 31.8 1.0
O C:ALA157 4.6 19.1 1.0
C9 C:VMY1271 4.6 28.8 1.0
F1 C:VMY1271 4.7 39.4 1.0
CE C:MET103 4.7 26.5 1.0
CB C:ALA157 4.7 18.3 1.0
O C:MET103 4.8 33.1 1.0
CA C:MET103 4.8 22.1 1.0

Fluorine binding site 7 out of 12 in 4bqp

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Fluorine binding site 7 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1271

b:29.7
occ:1.00
 F1 D:VMY1271 0.0 29.7 1.0
C13 D:VMY1271 1.4 31.0 1.0
C14 D:VMY1271 2.3 33.7 1.0
C12 D:VMY1271 2.4 29.1 1.0
C11 D:VMY1271 2.8 25.4 1.0
C D:ALA198 3.3 23.3 1.0
O D:ALA198 3.3 24.1 1.0
CB D:ALA198 3.4 19.9 1.0
N5 D:VMY1271 3.5 20.4 1.0
N D:MET199 3.6 20.3 1.0
C17 D:VMY1271 3.6 31.7 1.0
C15 D:VMY1271 3.6 33.8 1.0
N4 D:VMY1271 3.6 23.7 1.0
SD D:MET199 3.8 32.6 1.0
S D:VMY1271 3.9 21.6 1.0
CA D:MET199 3.9 20.8 1.0
S1 D:VMY1271 3.9 15.6 1.0
CA D:ALA198 4.0 19.3 1.0
C16 D:VMY1271 4.1 32.5 1.0
CG D:MET199 4.1 27.9 1.0
CB D:MET199 4.6 23.5 1.0
CE D:MET103 4.6 24.4 1.0
F D:VMY1271 4.7 31.6 1.0
CB D:ILE202 4.7 29.9 1.0
C2 D:VMY1271 4.7 22.0 1.0
C8 D:VMY1271 4.8 18.3 1.0
C10 D:VMY1271 5.0 22.4 1.0

Fluorine binding site 8 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 8 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1271

b:31.6
occ:1.00
 F D:VMY1271 0.0 31.6 1.0
C17 D:VMY1271 1.4 31.7 1.0
C16 D:VMY1271 2.3 32.5 1.0
C12 D:VMY1271 2.3 29.1 1.0
C11 D:VMY1271 2.8 25.4 1.0
CA D:GLY104 2.9 17.9 1.0
N4 D:VMY1271 3.2 23.7 1.0
C10 D:VMY1271 3.4 22.4 1.0
N D:GLY104 3.4 17.2 1.0
CD2 D:LEU207 3.4 33.2 1.0
C13 D:VMY1271 3.6 31.0 1.0
C15 D:VMY1271 3.6 33.8 1.0
C D:MET103 3.9 19.7 1.0
O D:MET103 4.1 15.2 1.0
C14 D:VMY1271 4.1 33.7 1.0
C D:GLY104 4.2 21.6 1.0
N5 D:VMY1271 4.2 20.4 1.0
CG D:MET103 4.3 23.1 1.0
CB D:ALA157 4.4 14.2 1.0
O D:ALA157 4.4 13.5 1.0
C9 D:VMY1271 4.4 20.1 1.0
O D:GLY104 4.6 22.4 1.0
F1 D:VMY1271 4.7 29.7 1.0
CB D:ILE202 4.7 29.9 1.0
C8 D:VMY1271 4.8 18.3 1.0
CG D:LEU207 4.9 30.1 1.0
CA D:MET103 4.9 16.2 1.0
C D:ALA157 4.9 15.3 1.0
CB D:MET103 5.0 19.2 1.0

Fluorine binding site 9 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 9 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1271

b:22.9
occ:1.00
 F1 E:VMY1271 0.0 22.9 1.0
C13 E:VMY1271 1.4 20.4 1.0
C12 E:VMY1271 2.3 18.3 1.0
C14 E:VMY1271 2.4 18.4 1.0
C11 E:VMY1271 2.8 19.4 1.0
C17 E:VMY1271 3.6 19.3 1.0
C15 E:VMY1271 3.6 21.1 1.0
N5 E:VMY1271 3.6 27.8 1.0
N4 E:VMY1271 3.7 26.8 1.0
O E:HOH2018 3.9 16.6 1.0
S E:VMY1271 4.1 20.1 1.0
C16 E:VMY1271 4.1 21.2 1.0
S1 E:VMY1271 4.1 22.5 1.0
O E:HOH2036 4.1 25.4 1.0
O E:HOH2042 4.3 20.6 1.0
F E:VMY1271 4.7 19.4 1.0
O E:HOH2017 4.9 21.8 1.0
CE E:MET103 5.0 19.6 1.0
C2 E:VMY1271 5.0 20.1 1.0

Fluorine binding site 10 out of 12 in 4bqp

Go back to Fluorine Binding Sites List in 4bqp
Fluorine binding site 10 out of 12 in the Mtb Inha Complex with Methyl-Thiazole Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Mtb Inha Complex with Methyl-Thiazole Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1271

b:19.4
occ:1.00
 F E:VMY1271 0.0 19.4 1.0
C17 E:VMY1271 1.4 19.3 1.0
C12 E:VMY1271 2.3 18.3 1.0
C16 E:VMY1271 2.4 21.2 1.0
C11 E:VMY1271 2.8 19.4 1.0
CA E:GLY104 3.0 20.2 1.0
N4 E:VMY1271 3.1 26.8 1.0
C10 E:VMY1271 3.2 26.0 1.0
CD2 E:LEU207 3.4 25.9 1.0
N E:GLY104 3.4 19.5 1.0
C13 E:VMY1271 3.6 20.4 1.0
C15 E:VMY1271 3.6 21.1 1.0
C E:MET103 3.9 23.2 1.0
N5 E:VMY1271 4.0 27.8 1.0
O E:MET103 4.1 23.3 1.0
C14 E:VMY1271 4.1 18.4 1.0
CG E:MET103 4.1 20.7 1.0
C9 E:VMY1271 4.2 28.2 1.0
C E:GLY104 4.3 21.8 1.0
OE1 E:GLN100 4.4 40.1 1.0
O E:ALA157 4.5 14.2 1.0
C8 E:VMY1271 4.7 28.7 1.0
F1 E:VMY1271 4.7 22.9 1.0
CB E:ALA157 4.7 16.7 1.0
O E:GLY104 4.8 21.7 1.0
CG E:LEU207 4.9 23.5 1.0
CB E:MET103 4.9 17.9 1.0
CA E:MET103 4.9 16.2 1.0

Reference:

P.S.Shirude, P.Madhavapeddi, M.Naik, K.Murugan, V.Shinde, R.Nandishaiah, J.Bhat, A.Kumar, S.Hameed, G.Holdgate, G.Davies, H.Mcmiken, N.Hegde, A.Ambady, J.Venkatraman, M.Panda, B.Bandodkar, V.K.Sambandamurthy, J.A.Read. Methyl-Thiazoles: A Novel Mode of Inhibition with the Potential to Develop Novel Inhibitors Targeting Inha in Mycobacterium Tuberculosis. J.Med.Chem. V. 56 8533 2013.
ISSN: ISSN 0022-2623
PubMed: 24107081
DOI: 10.1021/JM4012033
Page generated: Thu Aug 1 00:17:56 2024

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