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Sodium 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:

Fluorine (F) 3 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3kqd

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

b:59.4
occ:1.00
 O A:TYR185 2.3 55.0 1.0
O A:LYS224 2.4 46.4 1.0
O A:ARG222 3.0 51.9 1.0
C A:TYR185 3.5 54.4 1.0
C A:LYS224 3.6 45.9 1.0
C A:ARG222 3.8 52.7 1.0
OD1 A:ASP189 3.9 49.7 1.0
C A:ALA221 4.1 55.5 1.0
N A:LYS224 4.2 40.4 1.0
N A:TYR185 4.2 49.5 1.0
N A:ARG222 4.2 49.5 1.0
O A:ALA221 4.3 57.9 1.0
CA A:TYR185 4.3 49.0 1.0
CA A:ALA221 4.3 50.5 1.0
O A:LYS186 4.4 52.1 1.0
CA A:LYS224 4.4 39.7 1.0
N A:ASP185A 4.5 51.0 1.0
N A:TYR225 4.5 42.6 1.0
N A:LYS223 4.5 49.2 1.0
CA A:TYR225 4.6 42.4 1.0
O A:ASP185A 4.6 57.0 1.0
CA A:LYS223 4.6 48.1 1.0
CB A:TYR185 4.6 49.1 1.0
CA A:ASP185A 4.6 51.4 1.0
C A:ASP185A 4.6 56.3 1.0
CA A:ARG222 4.7 48.3 1.0
CD1 A:TYR225 4.7 48.5 1.0
N A:GLY223A 4.7 44.9 1.0
O A:HOH413 4.8 41.8 1.0
CG A:ASP189 4.8 50.8 1.0
C A:LYS223 4.9 49.5 1.0

Sodium binding site 2 out of 2 in 3kqd

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

b:59.4
occ:1.00
 O A:ASN72 2.2 64.1 1.0
OE2 A:GLU80 2.2 82.1 1.0
OD1 A:ASP70 2.4 76.6 1.0
O A:GLN75 2.5 78.4 1.0
CD A:GLU80 2.9 89.2 1.0
OE2 A:GLU77 3.0 0.6 1.0
OE1 A:GLU80 3.1 59.7 1.0
C A:ASN72 3.4 63.8 1.0
O A:HOH405 3.4 45.6 1.0
C A:GLN75 3.4 79.9 1.0
CG A:ASP70 3.5 73.0 1.0
CD A:GLU77 3.8 0.7 1.0
O A:THR73 3.9 67.8 1.0
CA A:GLU76 3.9 80.1 1.0
N A:GLU77 4.0 85.0 1.0
CG A:GLU77 4.0 97.9 1.0
N A:GLU76 4.0 79.0 1.0
CA A:THR73 4.1 61.5 1.0
N A:THR73 4.1 61.1 1.0
C A:THR73 4.2 68.0 1.0
OD2 A:ASP70 4.2 73.2 1.0
N A:ASN72 4.2 57.6 1.0
CG A:GLU80 4.2 75.7 1.0
CA A:ASN72 4.4 57.7 1.0
C A:GLU76 4.4 86.5 1.0
CB A:ASP70 4.5 59.1 1.0
N A:GLN75 4.5 74.2 1.0
CB A:GLU77 4.5 87.1 1.0
CA A:GLN75 4.5 74.7 1.0
CA A:ASP70 4.6 56.9 1.0
N A:ARG71 4.7 56.4 1.0
CB A:ASN72 4.8 54.5 1.0
CA A:GLU77 4.9 85.5 1.0
CB A:GLU80 4.9 69.7 1.0
OE1 A:GLU77 5.0 0.4 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 11:14:29 2024

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