Atomistry » Fluorine » PDB 3jx3-3kql » 3kqb
Atomistry »
  Fluorine »
    PDB 3jx3-3kql »
      3kqb »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy