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Sodium 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:

Fluorine (F) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3kqb

Go back to Sodium Binding Sites List in 3kqb
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na302

b:41.3
occ:1.00
 O A:TYR185 2.2 39.1 1.0
O A:LYS224 2.2 34.4 1.0
O A:HOH419 2.4 34.6 1.0
O A:HOH466 2.5 42.0 1.0
O A:HOH445 2.8 35.7 1.0
O A:ARG222 2.8 39.0 1.0
C A:LYS224 3.3 35.0 1.0
C A:TYR185 3.4 39.8 1.0
C A:ARG222 3.8 39.3 1.0
N A:LYS224 3.9 34.8 1.0
N A:TYR185 4.1 33.0 1.0
CA A:LYS224 4.2 33.7 1.0
OD1 A:ASP189 4.2 31.5 1.0
C A:ALA221 4.2 36.9 1.0
CA A:TYR185 4.3 33.1 1.0
N A:TYR225 4.3 30.1 1.0
O A:ALA221 4.3 35.6 1.0
N A:ARG222 4.4 34.4 1.0
N A:ASP185A 4.4 38.8 1.0
O A:LYS186 4.4 38.1 1.0
CA A:TYR225 4.5 28.6 1.0
O A:ASP185A 4.5 46.5 1.0
CA A:ASP185A 4.5 40.3 1.0
CA A:ALA221 4.6 32.1 1.0
CD1 A:TYR225 4.6 35.4 1.0
N A:LYS223 4.6 35.5 1.0
N A:GLY223A 4.6 33.9 1.0
CA A:LYS223 4.6 35.0 1.0
C A:ASP185A 4.6 45.4 1.0
CB A:TYR185 4.8 32.7 1.0
CA A:ARG222 4.8 34.3 1.0
CB A:LYS224 4.8 35.0 1.0
C A:LYS223 4.8 37.4 1.0
O A:HOH424 4.8 29.7 1.0
CE1 A:TYR225 4.9 36.6 1.0
C A:GLY223A 5.0 38.4 1.0

Sodium binding site 2 out of 2 in 3kqb

Go back to Sodium Binding Sites List in 3kqb
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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:Na303

b:57.1
occ:1.00
 O A:ASN72 2.2 53.2 1.0
O A:GLN75 2.3 71.8 1.0
OD1 A:ASP70 2.4 48.7 1.0
OE2 A:GLU80 2.5 63.7 1.0
OE2 A:GLU77 3.0 86.1 1.0
CD A:GLU80 3.1 66.9 1.0
OE1 A:GLU80 3.1 53.2 1.0
C A:ASN72 3.3 52.5 1.0
C A:GLN75 3.4 72.7 1.0
CG A:ASP70 3.4 47.8 1.0
CD A:GLU77 3.7 0.6 1.0
CG A:GLU77 3.7 87.5 1.0
CA A:THR73 4.0 51.5 1.0
N A:THR73 4.0 50.2 1.0
OD2 A:ASP70 4.0 51.8 1.0
N A:GLU77 4.1 76.8 1.0
N A:GLU76 4.2 71.7 1.0
CA A:GLU76 4.3 72.8 1.0
C A:THR73 4.3 58.3 1.0
N A:ASN72 4.3 44.0 1.0
N A:GLN75 4.3 65.5 1.0
CA A:ASN72 4.3 45.5 1.0
CA A:GLN75 4.4 66.6 1.0
CG A:GLU80 4.4 53.3 1.0
CB A:GLU77 4.5 78.3 1.0
CB A:ASP70 4.5 39.2 1.0
O A:THR73 4.6 58.4 1.0
C A:GLU76 4.6 79.1 1.0
CA A:ASP70 4.6 37.1 1.0
OE1 A:GLU77 4.7 96.8 1.0
N A:GLU74 4.8 56.5 1.0
N A:ARG71 4.8 36.2 1.0
CB A:ASN72 4.8 45.1 1.0
CA A:GLU77 4.9 77.0 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: Mon Oct 7 11:14:18 2024

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