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Fluorine in PDB 4unq: Mtb Tmk in Complex with Compound 36

Enzymatic activity of Mtb Tmk in Complex with Compound 36

All present enzymatic activity of Mtb Tmk in Complex with Compound 36:
2.7.4.9;

Protein crystallography data

The structure of Mtb Tmk in Complex with Compound 36, PDB code: 4unq was solved by J.A.Read, S.Hussein, H.Gingell, J.Tucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.36 / 2.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 75.459, 75.459, 71.579, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 21.3

Other elements in 4unq:

The structure of Mtb Tmk in Complex with Compound 36 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mtb Tmk in Complex with Compound 36 (pdb code 4unq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Mtb Tmk in Complex with Compound 36, PDB code: 4unq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 1 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1210

b:51.2
occ:1.00
 F21 A:H6D1210 0.0 51.2 1.0
C20 A:H6D1210 1.3 50.1 1.0
O19 A:H6D1210 2.1 45.2 1.0
F23 A:H6D1210 2.1 53.1 1.0
F22 A:H6D1210 2.2 52.9 1.0
CD2 A:LEU52 3.4 44.6 1.0
C17 A:H6D1210 3.4 42.4 1.0
NH1 A:ARG107 3.6 64.9 1.0
CZ A:ARG107 3.7 63.4 1.0
NH2 A:ARG107 3.7 64.5 1.0
CD1 A:LEU52 4.1 46.0 1.0
C18 A:H6D1210 4.2 41.3 1.0
NE A:ARG107 4.3 58.9 1.0
CG A:LEU52 4.3 45.5 1.0
C16 A:H6D1210 4.4 39.6 1.0
CD2 A:LEU171 4.5 55.0 1.0
CG A:ARG107 4.8 43.4 1.0
CD A:ARG107 4.9 52.0 1.0

Fluorine binding site 2 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 2 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1210

b:52.9
occ:1.00
 F22 A:H6D1210 0.0 52.9 1.0
C20 A:H6D1210 1.3 50.1 1.0
F23 A:H6D1210 2.0 53.1 1.0
F21 A:H6D1210 2.2 51.2 1.0
O19 A:H6D1210 2.2 45.2 1.0
C17 A:H6D1210 2.8 42.4 1.0
C18 A:H6D1210 2.9 41.3 1.0
CD2 A:TYR103 3.8 34.0 1.0
C16 A:H6D1210 3.9 39.6 1.0
C13 A:H6D1210 4.1 39.9 1.0
CD2 A:LEU171 4.3 55.0 1.0
CB A:TYR103 4.3 30.4 1.0
CG A:TYR103 4.4 31.3 1.0
CD1 A:LEU52 4.6 46.0 1.0
CE2 A:TYR103 4.6 36.0 1.0
C5 A:H6D1210 4.8 40.8 1.0
C15 A:H6D1210 4.9 40.7 1.0
C6 A:H6D1210 4.9 40.6 1.0
CD2 A:LEU52 4.9 44.6 1.0
C14 A:H6D1210 5.0 41.7 1.0

Fluorine binding site 3 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 3 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1210

b:53.1
occ:1.00
 F23 A:H6D1210 0.0 53.1 1.0
C20 A:H6D1210 1.3 50.1 1.0
F22 A:H6D1210 2.0 52.9 1.0
F21 A:H6D1210 2.1 51.2 1.0
O19 A:H6D1210 2.2 45.2 1.0
C17 A:H6D1210 2.8 42.4 1.0
CG A:ARG107 3.1 43.4 1.0
C16 A:H6D1210 3.3 39.6 1.0
NE A:ARG107 3.7 58.9 1.0
CZ A:ARG107 3.7 63.4 1.0
C18 A:H6D1210 3.7 41.3 1.0
CD A:ARG107 3.8 52.0 1.0
NH1 A:ARG107 3.9 64.9 1.0
CD2 A:LEU171 4.0 55.0 1.0
CD1 A:LEU171 4.2 54.0 1.0
O A:TYR103 4.2 31.2 1.0
NH2 A:ARG107 4.3 64.5 1.0
CB A:ARG107 4.4 38.3 1.0
C15 A:H6D1210 4.5 40.7 1.0
CB A:TYR103 4.6 30.4 1.0
CD2 A:TYR103 4.7 34.0 1.0
CG A:LEU171 4.8 53.0 1.0
C13 A:H6D1210 4.8 39.9 1.0
C A:TYR103 4.8 30.7 1.0

Fluorine binding site 4 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 4 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1210

b:58.5
occ:1.00
 F21 B:H6D1210 0.0 58.5 1.0
C20 B:H6D1210 1.3 56.6 1.0
F22 B:H6D1210 2.1 56.1 1.0
O19 B:H6D1210 2.1 53.3 1.0
F23 B:H6D1210 2.2 55.4 1.0
C17 B:H6D1210 2.8 50.8 1.0
CG B:ARG107 2.8 46.4 1.0
C16 B:H6D1210 3.3 49.2 1.0
CD2 B:LEU171 3.4 43.7 1.0
NE B:ARG107 3.4 61.0 1.0
CD B:ARG107 3.6 54.3 1.0
C18 B:H6D1210 3.7 47.9 1.0
CZ B:ARG107 3.9 63.6 1.0
CB B:ARG107 4.1 42.2 1.0
CD1 B:LEU171 4.2 45.0 1.0
O B:TYR103 4.3 37.3 1.0
NH1 B:ARG107 4.3 63.5 1.0
CG B:LEU171 4.4 46.2 1.0
NH2 B:ARG107 4.4 64.8 1.0
C15 B:H6D1210 4.4 48.3 1.0
CB B:TYR103 4.7 34.5 1.0
C13 B:H6D1210 4.8 46.0 1.0
CD1 B:TYR103 4.8 38.2 1.0
C B:TYR103 4.9 35.3 1.0

Fluorine binding site 5 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 5 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1210

b:56.1
occ:1.00
 F22 B:H6D1210 0.0 56.1 1.0
C20 B:H6D1210 1.3 56.6 1.0
F23 B:H6D1210 2.1 55.4 1.0
F21 B:H6D1210 2.1 58.5 1.0
O19 B:H6D1210 2.2 53.3 1.0
CD2 B:LEU52 3.3 57.8 1.0
C17 B:H6D1210 3.5 50.8 1.0
CZ B:ARG107 3.7 63.6 1.0
NH2 B:ARG107 3.7 64.8 1.0
CD2 B:LEU171 3.9 43.7 1.0
NE B:ARG107 3.9 61.0 1.0
NH1 B:ARG107 4.1 63.5 1.0
C18 B:H6D1210 4.3 47.9 1.0
CD1 B:LEU52 4.3 54.6 1.0
CG B:LEU52 4.4 56.5 1.0
C16 B:H6D1210 4.4 49.2 1.0
CG B:ARG107 4.5 46.4 1.0
CD B:ARG107 4.6 54.3 1.0

Fluorine binding site 6 out of 6 in 4unq

Go back to Fluorine Binding Sites List in 4unq
Fluorine binding site 6 out of 6 in the Mtb Tmk in Complex with Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mtb Tmk in Complex with Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1210

b:55.4
occ:1.00
 F23 B:H6D1210 0.0 55.4 1.0
C20 B:H6D1210 1.3 56.6 1.0
F22 B:H6D1210 2.1 56.1 1.0
F21 B:H6D1210 2.2 58.5 1.0
O19 B:H6D1210 2.2 53.3 1.0
C17 B:H6D1210 2.8 50.8 1.0
C18 B:H6D1210 3.0 47.9 1.0
CD2 B:LEU171 3.6 43.7 1.0
C16 B:H6D1210 4.0 49.2 1.0
CD1 B:TYR103 4.0 38.2 1.0
C13 B:H6D1210 4.2 46.0 1.0
CB B:TYR103 4.5 34.5 1.0
CG B:TYR103 4.5 35.8 1.0
CD1 B:LEU52 4.6 54.6 1.0
CD2 B:LEU52 4.7 57.8 1.0
CE1 B:TYR103 4.7 38.9 1.0
O B:HOH2059 4.8 35.4 1.0
C5 B:H6D1210 4.8 43.0 1.0
CG B:LEU171 4.9 46.2 1.0
CG B:ARG107 4.9 46.4 1.0
C15 B:H6D1210 5.0 48.3 1.0

Reference:

M.Naik, A.Raichurkar, B.S.Bandodkar, B.V.Varun, S.Bhat, R.Kalkhambkar, K.Murugan, R.Menon, J.Bhat, B.Paul, H.Iyer, S.Hussein, J.A.Tucker, M.Vogtherr, K.J.Embrey, H.Mcmiken, S.Prasad, A.Gill, B.G.Ugarkar, J.Venkatraman, J.Read, M.Panda. Structure Guided Lead Generation For M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-One As Potent Inhibitors. J.Med.Chem. V. 58 753 2015.
ISSN: ISSN 0022-2623
PubMed: 25486447
DOI: 10.1021/JM5012947
Page generated: Thu Aug 1 06:08:44 2024

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