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

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

Resolution Low / High (Å) 38.40 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.700, 72.100, 76.800, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 25.4

Other elements in 3kqd:

The structure of Factor Xa in Complex with the Inhibitor 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-3-(Trifluoromethyl)-5,6-Dihydro- 1H-Pyrazolo[3,4-C]Pyridin-7(4H)- One (pdb code 3kqd). 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 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-3-(Trifluoromethyl)-5,6-Dihydro- 1H-Pyrazolo[3,4-C]Pyridin-7(4H)- One, PDB code: 3kqd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3kqd

Go back to Fluorine Binding Sites List in 3kqd
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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:49.9
occ:1.00
 F42 A:LGL301 0.0 49.9 1.0
C32 A:LGL301 1.4 47.5 1.0
F44 A:LGL301 2.1 43.8 1.0
F43 A:LGL301 2.2 47.6 1.0
C21 A:LGL301 2.4 45.0 1.0
N33 A:LGL301 2.7 41.5 1.0
O A:GLU146 3.5 59.7 1.0
NH2 A:ARG143 3.5 74.8 1.0
CB A:GLN192 3.7 41.0 1.0
SG A:CYS220 3.7 51.0 1.0
C16 A:LGL301 3.8 42.9 1.0
SG A:CYS191 3.8 50.9 1.0
NE A:ARG143 3.8 61.8 1.0
CZ A:ARG143 3.8 77.6 1.0
NE2 A:GLN192 4.0 72.9 1.0
N35 A:LGL301 4.0 39.3 1.0
CG A:GLU146 4.2 58.8 1.0
CD A:GLN192 4.3 78.6 1.0
C A:GLU146 4.4 61.0 1.0
N A:GLN192 4.4 41.7 1.0
CG A:GLN192 4.5 58.7 1.0
C20 A:LGL301 4.5 42.3 1.0
CA A:GLU146 4.6 52.8 1.0
CA A:GLN192 4.7 40.0 1.0
C25 A:LGL301 4.7 41.3 1.0
NH1 A:ARG143 4.7 50.6 1.0
CD A:ARG143 4.8 64.2 1.0
C18 A:LGL301 4.9 39.0 1.0
OE1 A:GLN192 5.0 73.1 1.0
CB A:GLU146 5.0 53.4 1.0

Fluorine binding site 2 out of 3 in 3kqd

Go back to Fluorine Binding Sites List in 3kqd
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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:47.6
occ:1.00
 F43 A:LGL301 0.0 47.6 1.0
C32 A:LGL301 1.4 47.5 1.0
F44 A:LGL301 2.2 43.8 1.0
F42 A:LGL301 2.2 49.9 1.0
C21 A:LGL301 2.4 45.0 1.0
C16 A:LGL301 3.1 42.9 1.0
NE2 A:GLN192 3.3 72.9 1.0
C25 A:LGL301 3.4 41.3 1.0
N33 A:LGL301 3.5 41.5 1.0
NH2 A:ARG143 3.9 74.8 1.0
CD A:GLN192 4.2 78.6 1.0
C20 A:LGL301 4.3 42.3 1.0
N35 A:LGL301 4.4 39.3 1.0
CZ A:ARG143 4.6 77.6 1.0
OE1 A:GLN192 4.7 73.1 1.0
CB A:GLN192 4.8 41.0 1.0
O A:GLU146 4.9 59.7 1.0
CG A:GLN192 4.9 58.7 1.0
C28 A:LGL301 5.0 42.3 1.0

Fluorine binding site 3 out of 3 in 3kqd

Go back to Fluorine Binding Sites List in 3kqd
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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 1-(3-(5-Oxo-4,5- Dihydro-1H-1, 2,4-Triazol-3-Yl)Phenyl)-6-(2'-(Pyrrolidin-1- Ylmethyl)Biphenyl-4- Yl)-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:43.8
occ:1.00
 F44 A:LGL301 0.0 43.8 1.0
C32 A:LGL301 1.4 47.5 1.0
F42 A:LGL301 2.1 49.9 1.0
F43 A:LGL301 2.2 47.6 1.0
C21 A:LGL301 2.4 45.0 1.0
C16 A:LGL301 3.2 42.9 1.0
N33 A:LGL301 3.3 41.5 1.0
CG A:GLU146 3.5 58.8 1.0
CA A:GLY218 3.6 45.1 1.0
C25 A:LGL301 3.7 41.3 1.0
OE2 A:GLU146 4.0 52.3 1.0
CD A:GLU146 4.1 67.4 1.0
N35 A:LGL301 4.2 39.3 1.0
C20 A:LGL301 4.3 42.3 1.0
C A:GLY218 4.3 51.0 1.0
N A:GLY218 4.3 44.3 1.0
SG A:CYS220 4.3 51.0 1.0
O A:GLU146 4.4 59.7 1.0
N A:CYS220 4.8 48.2 1.0
CB A:GLU146 4.8 53.4 1.0
O A:GLY218 4.8 50.8 1.0
NH2 A:ARG143 4.9 74.8 1.0
NH2 A:ARG222 4.9 80.9 1.0
C28 A:LGL301 4.9 42.3 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 17:22:23 2025

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