Atomistry » Sodium » PDB 3k9g-3la1 » 3kqc
Atomistry »
  Sodium »
    PDB 3k9g-3la1 »
      3kqc »

Sodium 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:

Fluorine (F) 3 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3kqc

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

b:41.5
occ:1.00
 O A:TYR185 2.2 36.5 1.0
O A:LYS224 2.2 35.1 1.0
O A:HOH421 2.3 30.2 1.0
O A:ARG222 2.6 38.0 1.0
O A:HOH456 2.9 37.5 1.0
C A:LYS224 3.3 34.9 1.0
C A:TYR185 3.5 38.9 1.0
C A:ARG222 3.7 38.1 1.0
N A:LYS224 3.8 34.5 1.0
CA A:LYS224 4.1 33.5 1.0
O A:ASP185A 4.2 46.7 1.0
C A:ALA221 4.2 35.6 1.0
N A:TYR185 4.2 33.7 1.0
OD1 A:ASP189 4.3 31.3 1.0
N A:TYR225 4.3 30.0 1.0
O A:ALA221 4.3 34.3 1.0
N A:ARG222 4.3 33.0 1.0
N A:ASP185A 4.4 38.5 1.0
CA A:TYR185 4.4 33.6 1.0
CA A:ASP185A 4.4 40.3 1.0
O A:LYS186 4.5 38.1 1.0
C A:ASP185A 4.5 46.3 1.0
CA A:TYR225 4.5 28.4 1.0
N A:LYS223 4.5 35.0 1.0
N A:GLY223A 4.5 32.8 1.0
CA A:ALA221 4.5 31.9 1.0
CA A:LYS223 4.6 34.9 1.0
CD1 A:TYR225 4.6 33.4 1.0
CB A:LYS224 4.6 35.2 1.0
CA A:ARG222 4.7 32.6 1.0
C A:LYS223 4.7 36.2 1.0
O A:HOH422 4.8 33.8 1.0
CB A:TYR185 4.9 33.3 1.0
CE1 A:TYR225 4.9 35.2 1.0
C A:GLY223A 4.9 38.4 1.0

Sodium binding site 2 out of 2 in 3kqc

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

b:47.8
occ:1.00
 O A:ASN72 2.2 44.2 1.0
OD1 A:ASP70 2.3 47.6 1.0
O A:GLN75 2.4 65.4 1.0
OE2 A:GLU80 2.4 49.7 1.0
OE2 A:GLU77 2.5 82.4 1.0
O A:HOH483 2.6 42.4 1.0
CD A:GLU80 3.0 65.1 1.0
OE1 A:GLU80 3.2 53.4 1.0
C A:ASN72 3.3 44.6 1.0
CG A:ASP70 3.3 47.2 1.0
CD A:GLU77 3.4 95.8 1.0
C A:GLN75 3.6 66.0 1.0
CG A:GLU77 3.6 81.7 1.0
N A:ASN72 4.0 38.4 1.0
N A:THR73 4.1 43.1 1.0
CB A:ASP70 4.1 37.7 1.0
CA A:THR73 4.2 44.3 1.0
OD2 A:ASP70 4.2 52.4 1.0
CA A:ASP70 4.2 35.2 1.0
N A:GLU77 4.2 69.8 1.0
CA A:ASN72 4.2 39.0 1.0
CB A:GLU77 4.3 71.6 1.0
N A:ARG71 4.3 33.2 1.0
CG A:GLU80 4.4 50.2 1.0
CA A:GLU76 4.4 66.2 1.0
N A:GLU76 4.5 65.3 1.0
OE1 A:GLU77 4.5 97.9 1.0
N A:GLN75 4.5 58.0 1.0
CA A:GLN75 4.6 59.3 1.0
C A:GLU76 4.6 71.8 1.0
C A:THR73 4.6 51.8 1.0
CB A:ASN72 4.7 40.0 1.0
C A:ASP70 4.7 38.5 1.0
CA A:GLU77 4.9 70.1 1.0
N A:GLU74 5.0 49.2 1.0
CB A:GLU80 5.0 43.3 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 Oct 7 11:14:28 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy