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

Enzymatic activity of Factor Xa in Complex with the Inhibitor 3-Methyl-1-(3-(5- Oxo-4,5- Dihydro-1H-1,2,4-Triazol-3-Yl)Phenyl)-6-(2'- (Pyrrolidin-1-Ylmethyl) Biphenyl-4-Yl)-5,6-Dihydro-1H- Pyrazolo[3,4-C]Pyridin-7(4H)-One

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

Resolution Low / High (Å) 36.10 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.700, 72.200, 77.800, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3kqe

Go back to Sodium Binding Sites List in 3kqe
Sodium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor 3-Methyl-1-(3-(5- Oxo-4,5- Dihydro-1H-1,2,4-Triazol-3-Yl)Phenyl)-6-(2'- (Pyrrolidin-1-Ylmethyl) Biphenyl-4-Yl)-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 3-Methyl-1-(3-(5- Oxo-4,5- Dihydro-1H-1,2,4-Triazol-3-Yl)Phenyl)-6-(2'- (Pyrrolidin-1-Ylmethyl) Biphenyl-4-Yl)-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:50.9
occ:1.00
 O A:TYR185 2.2 40.9 1.0
O A:LYS224 2.3 40.9 1.0
O A:HOH420 2.4 37.8 1.0
O A:ARG222 2.8 42.1 1.0
C A:LYS224 3.4 40.7 1.0
C A:TYR185 3.4 43.4 1.0
C A:ARG222 3.8 41.7 1.0
N A:LYS224 4.0 38.5 1.0
O A:ALA221 4.1 41.1 1.0
C A:ALA221 4.1 41.1 1.0
N A:TYR185 4.2 37.7 1.0
CA A:LYS224 4.2 38.1 1.0
OD1 A:ASP189 4.2 39.3 1.0
N A:ARG222 4.3 36.1 1.0
CA A:TYR185 4.3 37.1 1.0
N A:TYR225 4.3 36.0 1.0
N A:ASP185A 4.4 43.9 1.0
O A:ASP185A 4.4 51.2 1.0
O A:LYS186 4.4 40.0 1.0
CA A:ASP185A 4.4 45.8 1.0
N A:LYS223 4.5 38.5 1.0
C A:ASP185A 4.5 50.4 1.0
CA A:ALA221 4.5 37.5 1.0
CA A:TYR225 4.5 33.6 1.0
CA A:LYS223 4.5 38.7 1.0
N A:GLY223A 4.6 37.3 1.0
CA A:ARG222 4.7 35.0 1.0
O A:HOH436 4.7 39.4 1.0
CD1 A:TYR225 4.7 38.9 1.0
CB A:TYR185 4.7 36.3 1.0
CB A:LYS224 4.7 40.4 1.0
C A:LYS223 4.8 40.3 1.0

Sodium binding site 2 out of 2 in 3kqe

Go back to Sodium Binding Sites List in 3kqe
Sodium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor 3-Methyl-1-(3-(5- Oxo-4,5- Dihydro-1H-1,2,4-Triazol-3-Yl)Phenyl)-6-(2'- (Pyrrolidin-1-Ylmethyl) Biphenyl-4-Yl)-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 3-Methyl-1-(3-(5- Oxo-4,5- Dihydro-1H-1,2,4-Triazol-3-Yl)Phenyl)-6-(2'- (Pyrrolidin-1-Ylmethyl) Biphenyl-4-Yl)-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:55.5
occ:1.00
 O A:ASN72 2.2 55.6 1.0
OE2 A:GLU80 2.2 76.5 1.0
OD1 A:ASP70 2.3 60.6 1.0
O A:GLN75 2.5 78.2 1.0
CD A:GLU80 2.6 81.5 1.0
OE1 A:GLU80 2.7 76.7 1.0
OE2 A:GLU77 3.2 0.5 1.0
C A:ASN72 3.3 55.0 1.0
CG A:ASP70 3.4 59.0 1.0
C A:GLN75 3.5 78.3 1.0
CG A:GLU80 3.8 61.7 1.0
CD A:GLU77 4.0 0.6 1.0
CA A:THR73 4.0 54.2 1.0
N A:THR73 4.0 52.9 1.0
CG A:GLU77 4.1 95.3 1.0
N A:GLU77 4.1 81.1 1.0
OD2 A:ASP70 4.1 66.3 1.0
N A:ASN72 4.2 47.2 1.0
N A:GLU76 4.3 76.4 1.0
CA A:GLU76 4.3 77.0 1.0
C A:THR73 4.3 63.6 1.0
CA A:ASN72 4.3 48.2 1.0
CB A:ASP70 4.4 44.6 1.0
O A:THR73 4.4 64.9 1.0
N A:GLN75 4.4 71.1 1.0
CA A:GLN75 4.5 72.1 1.0
CA A:ASP70 4.5 42.0 1.0
N A:ARG71 4.6 40.3 1.0
CB A:GLU77 4.6 83.3 1.0
C A:GLU76 4.7 83.2 1.0
CB A:ASN72 4.9 47.0 1.0
N A:GLU74 5.0 62.0 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 11:15:01 2024

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