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Fluorine in PDB 3ffg: Factor Xa in Complex with the Inhibitor (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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: 3ffg was solved by R.A.Alexander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.46 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.900, 72.500, 78.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with the Inhibitor (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 3ffg). 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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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: 3ffg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3ffg

Go back to Fluorine Binding Sites List in 3ffg
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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:F1

b:24.4
occ:1.00
 F43 A:FFG1 0.0 24.4 1.0
C32 A:FFG1 1.3 22.8 1.0
F45 A:FFG1 2.2 24.6 1.0
F44 A:FFG1 2.2 24.9 1.0
C21 A:FFG1 2.3 19.8 1.0
C16 A:FFG1 2.9 18.8 1.0
C25 A:FFG1 3.1 19.0 1.0
O A:HOH378 3.2 46.0 1.0
OE1 A:GLN192 3.3 29.8 1.0
N33 A:FFG1 3.5 19.5 1.0
O A:HOH486 3.5 40.9 1.0
C20 A:FFG1 4.2 18.1 1.0
O A:HOH336 4.2 45.9 1.0
NH2 A:ARG143 4.2 29.1 1.0
CD A:GLN192 4.4 27.4 1.0
N35 A:FFG1 4.4 17.6 1.0
C27 A:FFG1 4.6 19.5 1.0
CZ A:ARG143 4.8 30.1 1.0
CB A:GLN192 4.9 17.7 1.0
O A:HOH467 5.0 33.9 1.0

Fluorine binding site 2 out of 3 in 3ffg

Go back to Fluorine Binding Sites List in 3ffg
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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:F1

b:24.9
occ:1.00
 F44 A:FFG1 0.0 24.9 1.0
C32 A:FFG1 1.3 22.8 1.0
F45 A:FFG1 2.1 24.6 1.0
F43 A:FFG1 2.2 24.4 1.0
C21 A:FFG1 2.3 19.8 1.0
N33 A:FFG1 3.1 19.5 1.0
C16 A:FFG1 3.2 18.8 1.0
CG A:GLU146 3.5 24.8 1.0
O A:HOH486 3.6 40.9 1.0
O A:HOH336 3.6 45.9 1.0
CA A:GLY218 3.7 15.9 1.0
C25 A:FFG1 3.8 19.0 1.0
CD A:GLU146 4.0 26.0 1.0
SG A:CYS220 4.1 17.0 1.0
OE2 A:GLU146 4.2 29.7 1.0
N35 A:FFG1 4.2 17.6 1.0
C A:GLY218 4.2 16.8 1.0
C20 A:FFG1 4.2 18.1 1.0
O A:HOH467 4.3 33.9 1.0
N A:GLY218 4.3 16.0 1.0
O A:GLU146 4.4 23.0 1.0
O A:GLY218 4.7 16.0 1.0
N A:CYS220 4.7 16.9 1.0
OE1 A:GLU146 4.8 24.7 1.0
C27 A:FFG1 4.9 19.5 1.0
CB A:GLU146 4.9 23.9 1.0
NH2 A:ARG143 4.9 29.1 1.0
OE1 A:GLN192 4.9 29.8 1.0

Fluorine binding site 3 out of 3 in 3ffg

Go back to Fluorine Binding Sites List in 3ffg
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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 (R)-6-(2'-((3- Hydroxypyrrolidin-1-Yl)Methyl)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:F1

b:24.6
occ:1.00
 F45 A:FFG1 0.0 24.6 1.0
C32 A:FFG1 1.3 22.8 1.0
F44 A:FFG1 2.1 24.9 1.0
F43 A:FFG1 2.2 24.4 1.0
C21 A:FFG1 2.3 19.8 1.0
N33 A:FFG1 2.7 19.5 1.0
NH2 A:ARG143 3.3 29.1 1.0
OE1 A:GLN192 3.5 29.8 1.0
O A:HOH486 3.6 40.9 1.0
O A:GLU146 3.6 23.0 1.0
CB A:GLN192 3.6 17.7 1.0
C16 A:FFG1 3.6 18.8 1.0
CZ A:ARG143 3.6 30.1 1.0
NE A:ARG143 3.9 29.7 1.0
N35 A:FFG1 4.0 17.6 1.0
SG A:CYS220 4.1 17.0 1.0
CD A:GLN192 4.2 27.4 1.0
SG A:CYS191 4.2 16.7 1.0
NH1 A:ARG143 4.3 30.3 1.0
CG A:GLU146 4.4 24.8 1.0
O A:HOH378 4.4 46.0 1.0
N A:GLN192 4.5 13.9 1.0
C20 A:FFG1 4.5 18.1 1.0
CG A:GLN192 4.5 22.0 1.0
C25 A:FFG1 4.6 19.0 1.0
C A:GLU146 4.6 23.2 1.0
CA A:GLN192 4.7 15.2 1.0
CD A:ARG143 4.8 29.2 1.0
CA A:GLU146 4.9 22.4 1.0
O A:HOH336 4.9 45.9 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 16:16:23 2025

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