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Fluorine in PDB 2fzz: Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One, PDB code: 2fzz was solved by R.S.Alexander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.95 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.300, 72.500, 79.300, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One (pdb code 2fzz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One, PDB code: 2fzz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2fzz

Go back to Fluorine Binding Sites List in 2fzz
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One


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 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:39.1
occ:1.00
 F A:5QC1 0.0 39.1 1.0
C10 A:5QC1 1.3 39.7 1.0
F2 A:5QC1 2.2 40.0 1.0
F1 A:5QC1 2.2 39.5 1.0
C7 A:5QC1 2.3 39.2 1.0
C8 A:5QC1 2.8 38.4 1.0
C31 A:5QC1 3.0 38.7 1.0
N3 A:5QC1 3.5 37.9 1.0
OE1 A:GLN192 3.8 46.8 1.0
C9 A:5QC1 4.1 37.9 1.0
CB A:GLN192 4.4 36.4 1.0
N2 A:5QC1 4.4 36.5 1.0
C29 A:5QC1 4.5 38.4 1.0
CG A:GLN192 4.6 40.0 1.0
CD A:GLN192 4.6 44.1 1.0
NE A:ARG143 4.8 43.9 1.0
O A:GLU146 4.8 41.1 1.0

Fluorine binding site 2 out of 3 in 2fzz

Go back to Fluorine Binding Sites List in 2fzz
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One


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 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:39.5
occ:1.00
 F1 A:5QC1 0.0 39.5 1.0
C10 A:5QC1 1.3 39.7 1.0
F A:5QC1 2.2 39.1 1.0
F2 A:5QC1 2.2 40.0 1.0
C7 A:5QC1 2.3 39.2 1.0
C8 A:5QC1 3.1 38.4 1.0
N3 A:5QC1 3.3 37.9 1.0
CG A:GLU146 3.4 40.9 1.0
C31 A:5QC1 3.5 38.7 1.0
OE2 A:GLU146 3.5 43.9 1.0
CD A:GLU146 3.7 40.4 1.0
CA A:GLY218 3.8 35.9 1.0
C9 A:5QC1 4.2 37.9 1.0
N2 A:5QC1 4.3 36.5 1.0
O A:GLU146 4.3 41.1 1.0
N A:GLY218 4.4 34.7 1.0
SG A:CYS220 4.5 34.9 1.0
C29 A:5QC1 4.5 38.4 1.0
C A:GLY218 4.6 36.2 1.0
OE1 A:GLU146 4.7 39.6 1.0
CB A:GLU146 4.7 39.5 1.0

Fluorine binding site 3 out of 3 in 2fzz

Go back to Fluorine Binding Sites List in 2fzz
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One


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 1-(3-Amino-1,2- Benzisoxazol-5-Yl)-6-(2'-(((3R)-3-Hydroxy-1-Pyrrolidinyl) Methyl)-4-Biphenylyl)-3-(Trifluoromethyl)-1,4,5,6- Tetrahydro-7H-Pyrazolo[3,4-C]Pyridin-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:40.0
occ:1.00
 F2 A:5QC1 0.0 40.0 1.0
C10 A:5QC1 1.4 39.7 1.0
F A:5QC1 2.2 39.1 1.0
F1 A:5QC1 2.2 39.5 1.0
C7 A:5QC1 2.4 39.2 1.0
N3 A:5QC1 2.8 37.9 1.0
O A:GLU146 3.3 41.1 1.0
CB A:GLN192 3.5 36.4 1.0
NE A:ARG143 3.6 43.9 1.0
C8 A:5QC1 3.7 38.4 1.0
CD A:ARG143 3.7 40.3 1.0
CG A:GLU146 3.9 40.9 1.0
SG A:CYS191 4.0 39.4 1.0
SG A:CYS220 4.2 34.9 1.0
N2 A:5QC1 4.2 36.5 1.0
C A:GLU146 4.3 40.6 1.0
N A:GLN192 4.4 33.1 1.0
CG A:GLN192 4.4 40.0 1.0
CA A:GLU146 4.4 39.8 1.0
OE1 A:GLN192 4.5 46.8 1.0
C31 A:5QC1 4.6 38.7 1.0
C9 A:5QC1 4.6 37.9 1.0
CA A:GLN192 4.6 32.3 1.0
CZ A:ARG143 4.6 46.8 1.0
CB A:GLU146 4.8 39.5 1.0
CD A:GLU146 4.9 40.4 1.0
CD A:GLN192 5.0 44.1 1.0

Reference:

D.J.Pinto, M.J.Orwat, M.L.Quan, Q.Han, R.A.Galemmo, E.Amparo, B.Wells, C.Ellis, M.Y.He, R.S.Alexander, K.A.Rossi, A.Smallwood, P.C.Wong, J.M.Luettgen, A.R.Rendina, R.M.Knabb, L.Mersinger, C.Kettner, S.Bai, K.He, R.R.Wexler, P.Y.Lam. 1-[3-Aminobenzisoxazol-5'-Yl]-3-Trifluoromethyl-6- [2'-(3-(R)-Hydroxy-N-Pyrrolidinyl)Methyl-[1,1']- Biphen-4-Yl]-1,4,5,6-Tetrahydropyrazolo-[3,4-C]- Pyridin-7-One (Bms-740808) A Highly Potent, Selective, Efficacious, and Orally Bioavailable Inhibitor of Blood Coagulation Factor Xa. Bioorg.Med.Chem.Lett. V. 16 4141 2006.
ISSN: ISSN 0960-894X
PubMed: 16730984
DOI: 10.1016/J.BMCL.2006.02.069
Page generated: Sun Dec 13 11:36:18 2020

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