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Fluorine in PDB 3kqc: Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One

Enzymatic activity of Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One, PDB code: 3kqc was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.39 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.500, 72.100, 77.500, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.4

Other elements in 3kqc:

The structure of Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One 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 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One (pdb code 3kqc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One, PDB code: 3kqc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3kqc

Go back to Fluorine Binding Sites List in 3kqc
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


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 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:37.1
occ:1.00
 F39 A:LGK301 0.0 37.1 1.0
C28 A:LGK301 1.4 40.4 1.0
F40 A:LGK301 2.2 41.8 1.0
F41 A:LGK301 2.2 45.6 1.0
C21 A:LGK301 2.4 36.4 1.0
OE1 A:GLN192 2.8 70.6 1.0
C16 A:LGK301 3.1 34.6 1.0
C25 A:LGK301 3.4 35.6 1.0
N29 A:LGK301 3.5 34.6 1.0
CD A:GLN192 3.9 71.2 1.0
NH2 A:ARG143 3.9 30.6 1.0
C20 A:LGK301 4.3 34.0 1.0
N31 A:LGK301 4.4 30.9 1.0
CZ A:ARG143 4.4 56.5 1.0
CB A:GLN192 4.6 25.9 1.0
NE2 A:GLN192 4.6 67.4 1.0
NH1 A:ARG143 4.8 34.9 1.0
O A:GLU146 4.8 43.4 1.0
CG A:GLN192 4.9 38.8 1.0
C26 A:LGK301 4.9 37.7 1.0

Fluorine binding site 2 out of 3 in 3kqc

Go back to Fluorine Binding Sites List in 3kqc
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


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 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:41.8
occ:1.00
 F40 A:LGK301 0.0 41.8 1.0
C28 A:LGK301 1.4 40.4 1.0
F41 A:LGK301 2.1 45.6 1.0
F39 A:LGK301 2.2 37.1 1.0
C21 A:LGK301 2.4 36.4 1.0
C16 A:LGK301 3.2 34.6 1.0
N29 A:LGK301 3.3 34.6 1.0
CG A:GLU146 3.6 41.1 1.0
C25 A:LGK301 3.7 35.6 1.0
CA A:GLY218 3.9 27.8 1.0
O A:GLU146 4.2 43.4 1.0
CD A:GLU146 4.2 50.1 1.0
SG A:CYS220 4.3 32.6 1.0
N31 A:LGK301 4.3 30.9 1.0
C20 A:LGK301 4.3 34.0 1.0
C A:GLY218 4.3 34.9 1.0
OE2 A:GLU146 4.4 49.5 1.0
N A:GLY218 4.6 26.0 1.0
NH2 A:ARG143 4.6 30.6 1.0
OE1 A:GLN192 4.7 70.6 1.0
O A:GLY218 4.8 35.2 1.0
N A:CYS220 4.8 30.3 1.0
CB A:GLU146 4.8 36.5 1.0
C A:GLU146 5.0 43.1 1.0
C26 A:LGK301 5.0 37.7 1.0
CA A:GLU146 5.0 35.2 1.0

Fluorine binding site 3 out of 3 in 3kqc

Go back to Fluorine Binding Sites List in 3kqc
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


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 6-(2'- (Methylsulfonyl) Biphenyl-4-Yl)-1-(3-(5-Oxo-4,5-Dihydro-1H- 1,2,4-Triazol-3-Yl) Phenyl)-3-(Trifluoromethyl)-5,6- Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:45.6
occ:1.00
 F41 A:LGK301 0.0 45.6 1.0
C28 A:LGK301 1.4 40.4 1.0
F40 A:LGK301 2.1 41.8 1.0
F39 A:LGK301 2.2 37.1 1.0
C21 A:LGK301 2.4 36.4 1.0
N29 A:LGK301 2.7 34.6 1.0
NH2 A:ARG143 3.4 30.6 1.0
OE1 A:GLN192 3.4 70.6 1.0
O A:GLU146 3.5 43.4 1.0
CB A:GLN192 3.5 25.9 1.0
CZ A:ARG143 3.6 56.5 1.0
C16 A:LGK301 3.7 34.6 1.0
NE A:ARG143 3.7 51.4 1.0
SG A:CYS220 3.7 32.6 1.0
SG A:CYS191 3.9 32.6 1.0
N31 A:LGK301 4.0 30.9 1.0
CD A:GLN192 4.1 71.2 1.0
N A:GLN192 4.3 26.3 1.0
CG A:GLU146 4.4 41.1 1.0
NH1 A:ARG143 4.4 34.9 1.0
CG A:GLN192 4.4 38.8 1.0
C A:GLU146 4.5 43.1 1.0
C20 A:LGK301 4.5 34.0 1.0
CA A:GLN192 4.6 24.3 1.0
CD A:ARG143 4.7 47.7 1.0
C25 A:LGK301 4.7 35.6 1.0
CA A:GLU146 4.7 35.2 1.0
C17 A:LGK301 5.0 24.7 1.0
NE2 A:GLN192 5.0 67.4 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: Mon Jul 14 17:21:31 2025

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