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Fluorine in PDB 3kqb: Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide

Enzymatic activity of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide

All present enzymatic activity of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide, PDB code: 3kqb was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.85 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.700, 72.300, 77.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.1

Other elements in 3kqb:

The structure of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide (pdb code 3kqb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide, PDB code: 3kqb:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3kqb

Go back to Fluorine Binding Sites List in 3kqb
Fluorine binding site 1 out of 4 in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:45.3
occ:1.00
 F37 A:LGJ301 0.0 45.3 1.0
C18 A:LGJ301 1.3 37.3 1.0
C10 A:LGJ301 2.3 33.0 1.0
C17 A:LGJ301 2.4 35.5 1.0
N32 A:LGJ301 2.8 35.3 1.0
O A:GLY216 3.0 32.6 1.0
O A:HOH434 3.4 36.4 1.0
CA A:GLU217 3.6 28.9 1.0
C13 A:LGJ301 3.6 31.9 1.0
C8 A:LGJ301 3.7 33.7 1.0
CG A:GLU217 3.7 34.0 1.0
C A:GLY216 3.7 32.5 1.0
C24 A:LGJ301 4.0 35.5 1.0
N A:GLU217 4.0 29.5 1.0
CE2 A:PHE174 4.1 42.8 1.0
C5 A:LGJ301 4.1 32.6 1.0
CE3 A:TRP215 4.2 26.1 1.0
CB A:GLU217 4.2 29.2 1.0
O34 A:LGJ301 4.6 37.5 1.0
CZ3 A:TRP215 4.6 27.6 1.0
CZ A:PHE174 4.6 41.1 1.0
O35 A:LGJ301 4.7 41.9 1.0
N A:GLY218 4.7 29.4 1.0
CD2 A:PHE174 4.8 39.9 1.0
C A:GLU217 4.8 33.2 1.0
C14 A:LGJ301 4.8 34.3 1.0
C20 A:LGJ301 4.9 34.1 1.0
CA A:GLY216 4.9 27.6 1.0
N A:GLY216 4.9 27.9 1.0

Fluorine binding site 2 out of 4 in 3kqb

Go back to Fluorine Binding Sites List in 3kqb
Fluorine binding site 2 out of 4 in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:35.0
occ:1.00
 F38 A:LGJ301 0.0 35.0 1.0
C26 A:LGJ301 1.4 37.0 1.0
F39 A:LGJ301 2.1 42.2 1.0
F40 A:LGJ301 2.2 34.7 1.0
C21 A:LGJ301 2.4 33.7 1.0
N27 A:LGJ301 3.3 29.9 1.0
C12 A:LGJ301 3.3 31.8 1.0
CG A:GLU146 3.5 44.8 1.0
CA A:GLY218 4.0 30.7 1.0
O A:GLU146 4.1 43.8 1.0
CD A:GLU146 4.2 51.1 1.0
SG A:CYS220 4.3 31.5 1.0
N29 A:LGJ301 4.3 29.6 1.0
C20 A:LGJ301 4.4 34.1 1.0
OE2 A:GLU146 4.4 51.0 1.0
O A:HOH434 4.4 36.4 1.0
C A:GLY218 4.5 35.2 1.0
NH2 A:ARG143 4.5 39.0 1.0
OE1 A:GLN192 4.7 68.9 1.0
CB A:GLU146 4.7 37.3 1.0
N A:GLY218 4.7 29.4 1.0
C A:GLU146 4.8 43.5 1.0
N A:CYS220 4.8 31.1 1.0
CA A:GLU146 4.8 36.3 1.0
O A:GLY218 5.0 34.7 1.0

Fluorine binding site 3 out of 4 in 3kqb

Go back to Fluorine Binding Sites List in 3kqb
Fluorine binding site 3 out of 4 in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:42.2
occ:1.00
 F39 A:LGJ301 0.0 42.2 1.0
C26 A:LGJ301 1.4 37.0 1.0
F38 A:LGJ301 2.1 35.0 1.0
F40 A:LGJ301 2.2 34.7 1.0
C21 A:LGJ301 2.4 33.7 1.0
N27 A:LGJ301 2.7 29.9 1.0
OE1 A:GLN192 3.2 68.9 1.0
NH2 A:ARG143 3.4 39.0 1.0
O A:GLU146 3.5 43.8 1.0
CB A:GLN192 3.5 26.5 1.0
CZ A:ARG143 3.5 62.3 1.0
NE A:ARG143 3.6 54.5 1.0
C12 A:LGJ301 3.7 31.8 1.0
SG A:CYS191 3.8 31.4 1.0
SG A:CYS220 3.9 31.5 1.0
N29 A:LGJ301 4.0 29.6 1.0
CD A:GLN192 4.1 72.4 1.0
NH1 A:ARG143 4.3 40.2 1.0
N A:GLN192 4.3 26.1 1.0
CG A:GLN192 4.4 43.0 1.0
CD A:ARG143 4.5 49.7 1.0
CG A:GLU146 4.5 44.8 1.0
C A:GLU146 4.5 43.5 1.0
C20 A:LGJ301 4.6 34.1 1.0
CA A:GLN192 4.6 25.1 1.0
CA A:GLU146 4.7 36.3 1.0
C16 A:LGJ301 5.0 25.7 1.0

Fluorine binding site 4 out of 4 in 3kqb

Go back to Fluorine Binding Sites List in 3kqb
Fluorine binding site 4 out of 4 in the Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Factor Xa in Complex with the Inhibitor N-(3-Fluoro-2'- (Methylsulfonyl)Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4- Triazol-3-Yl)Phenyl)-3-(Trifluoromethyl)-1H- Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:34.7
occ:1.00
 F40 A:LGJ301 0.0 34.7 1.0
C26 A:LGJ301 1.4 37.0 1.0
F38 A:LGJ301 2.2 35.0 1.0
F39 A:LGJ301 2.2 42.2 1.0
C21 A:LGJ301 2.4 33.7 1.0
OE1 A:GLN192 2.8 68.9 1.0
C12 A:LGJ301 3.0 31.8 1.0
N27 A:LGJ301 3.5 29.9 1.0
NH2 A:ARG143 4.0 39.0 1.0
CD A:GLN192 4.1 72.4 1.0
C20 A:LGJ301 4.2 34.1 1.0
N29 A:LGJ301 4.4 29.6 1.0
CZ A:ARG143 4.4 62.3 1.0
CB A:GLN192 4.7 26.5 1.0
NH1 A:ARG143 4.7 40.2 1.0
O A:GLU146 4.8 43.8 1.0
CG A:GLN192 4.8 43.0 1.0

Reference:

M.L.Quan, D.J.Pinto, K.A.Rossi, S.Sheriff, R.S.Alexander, E.Amparo, K.Kish, R.M.Knabb, J.M.Luettgen, P.Morin, A.Smallwood, F.J.Woerner, R.R.Wexler. Phenyltriazolinones As Potent Factor Xa Inhibitors. Bioorg.Med.Chem.Lett. V. 20 1373 2010.
ISSN: ISSN 0960-894X
PubMed: 20100660
DOI: 10.1016/J.BMCL.2010.01.011
Page generated: Wed Jul 31 19:55:49 2024

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