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Fluorine in PDB 6yap: Crystal Structure of ZMCKO4A in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea

Enzymatic activity of Crystal Structure of ZMCKO4A in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea

All present enzymatic activity of Crystal Structure of ZMCKO4A 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 Structure of ZMCKO4A in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea, PDB code: 6yap 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) 27.81 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.670, 79.670, 203.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.2

Other elements in 6yap:

The structure of Crystal Structure of ZMCKO4A 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 Structure of ZMCKO4A in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea (pdb code 6yap). 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 Structure of ZMCKO4A in Complex with Inhibitor 1-(3-Chloro-5- Trifluoromethoxy-Phenyl)-3-[2-(2-Hydroxy-Ethyl)-Phenyl]-Urea, PDB code: 6yap:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6yap

Go back to Fluorine Binding Sites List in 6yap
Fluorine binding site 1 out of 3 in the Crystal Structure of ZMCKO4A 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 Structure of ZMCKO4A 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:F604

b:78.1
occ:1.00
 F2 A:OHZ604 0.0 78.1 1.0
C6 A:OHZ604 1.4 78.0 1.0
F A:OHZ604 2.2 78.5 1.0
O1 A:OHZ604 2.3 71.3 1.0
F1 A:OHZ604 2.3 83.3 1.0
C5 A:OHZ604 2.9 62.8 1.0
C7 A:OHZ604 3.1 54.8 1.0
C7M A:FAD603 3.4 45.0 1.0
CG1 A:VAL370 3.7 48.4 1.0
CZ3 A:TRP383 3.8 55.4 1.0
CH2 A:TRP389 3.8 44.8 1.0
CH2 A:TRP383 4.0 55.8 1.0
CZ2 A:TRP389 4.2 45.9 1.0
C4 A:OHZ604 4.2 63.4 1.0
C1 A:OHZ604 4.4 51.6 1.0
O A:OHZ604 4.5 50.5 1.0
C7 A:FAD603 4.5 39.2 1.0
C6 A:FAD603 4.7 35.7 1.0
CZ A:PHE57 4.7 44.9 1.0
CZ3 A:TRP389 4.9 44.2 1.0
CE3 A:TRP383 5.0 54.5 1.0

Fluorine binding site 2 out of 3 in 6yap

Go back to Fluorine Binding Sites List in 6yap
Fluorine binding site 2 out of 3 in the Crystal Structure of ZMCKO4A 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 Structure of ZMCKO4A 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:F604

b:78.5
occ:1.00
 F A:OHZ604 0.0 78.5 1.0
C6 A:OHZ604 1.4 78.0 1.0
F1 A:OHZ604 2.2 83.3 1.0
F2 A:OHZ604 2.2 78.1 1.0
O1 A:OHZ604 2.2 71.3 1.0
CD1 A:LEU377 3.4 65.9 1.0
C5 A:OHZ604 3.6 62.8 1.0
CZ3 A:TRP383 3.6 55.4 1.0
O A:HOH883 3.8 81.9 1.0
O A:HOH768 4.2 58.2 1.0
CE3 A:TRP383 4.3 54.5 1.0
C7 A:OHZ604 4.3 54.8 1.0
CH2 A:TRP383 4.5 55.8 1.0
C4 A:OHZ604 4.5 63.4 1.0
CZ2 A:TRP389 4.5 45.9 1.0
CH2 A:TRP389 4.8 44.8 1.0
CG A:LEU377 4.9 66.3 1.0

Fluorine binding site 3 out of 3 in 6yap

Go back to Fluorine Binding Sites List in 6yap
Fluorine binding site 3 out of 3 in the Crystal Structure of ZMCKO4A 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 Structure of ZMCKO4A 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:F604

b:83.3
occ:1.00
 F1 A:OHZ604 0.0 83.3 1.0
C6 A:OHZ604 1.4 78.0 1.0
F A:OHZ604 2.2 78.5 1.0
O1 A:OHZ604 2.2 71.3 1.0
F2 A:OHZ604 2.3 78.1 1.0
C5 A:OHZ604 2.8 62.8 1.0
CZ2 A:TRP389 3.0 45.9 1.0
C7 A:OHZ604 3.0 54.8 1.0
CH2 A:TRP389 3.2 44.8 1.0
C4 A:OHZ604 4.0 63.4 1.0
CE2 A:TRP389 4.3 46.2 1.0
C1 A:OHZ604 4.4 51.6 1.0
O A:HOH883 4.4 81.9 1.0
O A:OHZ604 4.5 50.5 1.0
CZ3 A:TRP389 4.5 44.2 1.0
CD A:PRO421 4.6 54.2 1.0
CB A:LEU452 4.6 39.8 1.0
CG A:PRO421 4.8 58.3 1.0
O A:LEU452 4.8 46.8 1.0
CD1 A:LEU452 4.9 45.0 1.0
C7M A:FAD603 5.0 45.0 1.0
NE1 A:TRP389 5.0 43.7 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: Tue Jul 15 17:39:44 2025

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