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Fluorine in PDB 6yaq: Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea

Enzymatic activity of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea

All present enzymatic activity of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea:
1.5.99.12;

Protein crystallography data

The structure of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea, PDB code: 6yaq was solved by D.Kopecny, P.Briozzo, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.95
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 101.518, 101.518, 128.171, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21

Other elements in 6yaq:

The structure of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea (pdb code 6yaq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea, PDB code: 6yaq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6yaq

Go back to Fluorine Binding Sites List in 6yaq
Fluorine binding site 1 out of 3 in the Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:57.8
occ:1.00
 F2 A:OHZ601 0.0 57.8 1.0
C6 A:OHZ601 1.3 54.6 1.0
F A:OHZ601 2.1 54.6 1.0
F1 A:OHZ601 2.1 52.9 1.0
O1 A:OHZ601 2.2 51.5 1.0
C5 A:OHZ601 2.8 46.4 1.0
C4 A:OHZ601 3.2 44.3 1.0
CZ3 A:TRP382 3.5 29.1 1.0
CD1 A:LEU376 3.5 30.0 1.0
O A:HOH1008 3.7 53.3 1.0
CG1 A:VAL369 3.9 24.9 1.0
C7 A:OHZ601 4.0 42.4 1.0
CB A:GLU372 4.0 28.6 1.0
CH2 A:TRP382 4.3 29.6 1.0
O A:HOH1089 4.4 51.7 1.0
CE3 A:TRP382 4.5 27.6 1.0
C3 A:OHZ601 4.5 45.6 1.0
N A:GLU373 4.8 23.7 1.0
C A:GLU372 4.8 27.7 1.0
CG A:GLU372 4.9 43.8 1.0
OE2 A:GLU372 4.9 85.1 1.0
CG A:LEU376 5.0 30.9 1.0

Fluorine binding site 2 out of 3 in 6yaq

Go back to Fluorine Binding Sites List in 6yaq
Fluorine binding site 2 out of 3 in the Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:54.6
occ:1.00
 F A:OHZ601 0.0 54.6 1.0
C6 A:OHZ601 1.3 54.6 1.0
F2 A:OHZ601 2.1 57.8 1.0
F1 A:OHZ601 2.1 52.9 1.0
O1 A:OHZ601 2.2 51.5 1.0
O A:HOH981 3.5 35.5 1.0
C5 A:OHZ601 3.5 46.4 1.0
CZ3 A:TRP382 3.7 29.1 1.0
CD1 A:LEU376 3.7 30.0 1.0
O A:HOH1089 3.9 51.7 1.0
O A:HOH757 4.2 29.7 1.0
CZ2 A:TRP388 4.3 24.1 1.0
CE3 A:TRP382 4.3 27.6 1.0
C7 A:OHZ601 4.3 42.4 1.0
C4 A:OHZ601 4.4 44.3 1.0
CH2 A:TRP382 4.4 29.6 1.0
CH2 A:TRP388 4.6 24.5 1.0
O A:HOH1008 4.6 53.3 1.0

Fluorine binding site 3 out of 3 in 6yaq

Go back to Fluorine Binding Sites List in 6yaq
Fluorine binding site 3 out of 3 in the Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Sttructure of ZMCKO8 in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:52.9
occ:1.00
 F1 A:OHZ601 0.0 52.9 1.0
C6 A:OHZ601 1.3 54.6 1.0
F2 A:OHZ601 2.1 57.8 1.0
F A:OHZ601 2.1 54.6 1.0
O1 A:OHZ601 2.2 51.5 1.0
C5 A:OHZ601 2.8 46.4 1.0
C7 A:OHZ601 3.2 42.4 1.0
CZ3 A:TRP382 3.5 29.1 1.0
CH2 A:TRP382 3.6 29.6 1.0
C7M A:FAD602 3.7 21.0 1.0
C4 A:OHZ601 3.8 44.3 1.0
CG1 A:VAL369 3.9 24.9 1.0
CH2 A:TRP388 4.2 24.5 1.0
C1 A:OHZ601 4.4 38.7 1.0
CZ2 A:TRP388 4.6 24.1 1.0
O A:OHZ601 4.6 35.9 1.0
CE3 A:TRP382 4.7 27.6 1.0
CZ2 A:TRP382 4.8 28.4 1.0
C7 A:FAD602 4.8 21.3 1.0
C3 A:OHZ601 4.9 45.6 1.0
C6 A:FAD602 5.0 23.2 1.0

Reference:

J.Nisler, D.Kopecny, Z.Pekna, R.Koncitikova, R.Koprna, N.Murvanidze, S.P.O.Werbrouck, L.Havlicek, N.De Diego, M.Kopecna, Z.Wimmer, P.Briozzo, S.Morera, D.Zalabak, L.Spichal, M.Strnad. Diphenylurea-Derived Cytokinin Oxidase/Dehydrogenase Inhibitors For Biotechnology and Agriculture. J.Exp.Bot. 2020.
ISSN: ESSN 1460-2431
PubMed: 32945834
DOI: 10.1093/JXB/ERAA437
Page generated: Fri Aug 2 04:27:52 2024

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