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Fluorine in PDB 2g00: Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide

Enzymatic activity of Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide

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

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide, PDB code: 2g00 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) 19.92 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.600, 72.400, 78.900, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 28.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide (pdb code 2g00). 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 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide, PDB code: 2g00:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2g00

Go back to Fluorine Binding Sites List in 2g00
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide


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 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:34.5
occ:1.00
F A:4QC711 0.0 34.5 1.0
C10 A:4QC711 1.3 34.4 1.0
F2 A:4QC711 2.1 35.1 1.0
F1 A:4QC711 2.2 33.7 1.0
C7 A:4QC711 2.3 34.6 1.0
C8 A:4QC711 3.0 35.2 1.0
CG A:GLU146 3.2 33.7 1.0
C24 A:4QC711 3.3 36.0 1.0
N3 A:4QC711 3.4 33.1 1.0
CD A:GLU146 3.5 32.5 1.0
OE2 A:GLU146 3.6 32.7 1.0
CA A:GLY218 3.7 27.5 1.0
OE1 A:GLU146 4.2 32.3 1.0
C9 A:4QC711 4.2 35.2 1.0
C A:GLY218 4.3 27.9 1.0
O A:GLU146 4.3 37.2 1.0
N2 A:4QC711 4.4 31.5 1.0
SG A:CYS220 4.4 29.3 1.0
N A:GLY218 4.4 27.1 1.0
CB A:GLU146 4.6 34.9 1.0
O A:GLY218 4.6 26.6 1.0
NZ A:LYS147 4.8 47.1 1.0
N A:CYS220 4.8 29.1 1.0
C12 A:4QC711 4.8 35.3 1.0
NE2 A:GLN192 5.0 38.0 1.0

Fluorine binding site 2 out of 3 in 2g00

Go back to Fluorine Binding Sites List in 2g00
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide


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 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:33.7
occ:1.00
F1 A:4QC711 0.0 33.7 1.0
C10 A:4QC711 1.3 34.4 1.0
F A:4QC711 2.2 34.5 1.0
F2 A:4QC711 2.2 35.1 1.0
C7 A:4QC711 2.4 34.6 1.0
C8 A:4QC711 3.0 35.2 1.0
NE2 A:GLN192 3.1 38.0 1.0
C24 A:4QC711 3.3 36.0 1.0
N3 A:4QC711 3.5 33.1 1.0
NH1 A:ARG143 4.0 33.0 1.0
C9 A:4QC711 4.2 35.2 1.0
CD A:GLN192 4.4 35.5 1.0
C12 A:4QC711 4.4 35.3 1.0
N2 A:4QC711 4.5 31.5 1.0
O A:GLU146 4.5 37.2 1.0
CZ A:ARG143 4.6 31.7 1.0
NZ A:LYS147 4.6 47.1 1.0
CB A:GLN192 4.7 27.3 1.0
NH2 A:ARG143 4.8 34.1 1.0
CG A:GLU146 4.8 33.7 1.0

Fluorine binding site 3 out of 3 in 2g00

Go back to Fluorine Binding Sites List in 2g00
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide


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 3-(6-(2'-((Dimethylamino) Methyl)-4-Biphenylyl)-7-Oxo-3-(Trifluoromethyl)-4,5,6,7-Tetrahydro- 1H-Pyrazolo[3,4-C]Pyridin-1-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:35.1
occ:1.00
F2 A:4QC711 0.0 35.1 1.0
C10 A:4QC711 1.3 34.4 1.0
F A:4QC711 2.1 34.5 1.0
F1 A:4QC711 2.2 33.7 1.0
C7 A:4QC711 2.3 34.6 1.0
N3 A:4QC711 2.8 33.1 1.0
O A:GLU146 3.2 37.2 1.0
NH1 A:ARG143 3.4 33.0 1.0
CG A:GLU146 3.5 33.7 1.0
C8 A:4QC711 3.6 35.2 1.0
NE2 A:GLN192 3.7 38.0 1.0
SG A:CYS220 3.8 29.3 1.0
SG A:CYS191 3.9 33.7 1.0
CB A:GLN192 4.0 27.3 1.0
C A:GLU146 4.1 36.8 1.0
CZ A:ARG143 4.1 31.7 1.0
N2 A:4QC711 4.2 31.5 1.0
CA A:GLU146 4.2 35.1 1.0
CD A:ARG143 4.4 27.1 1.0
CB A:GLU146 4.4 34.9 1.0
NE A:ARG143 4.5 30.0 1.0
CD A:GLU146 4.5 32.5 1.0
C24 A:4QC711 4.5 36.0 1.0
C9 A:4QC711 4.6 35.2 1.0
N A:GLN192 4.6 25.4 1.0
CD A:GLN192 4.8 35.5 1.0
NH2 A:ARG143 4.9 34.1 1.0
NZ A:LYS147 4.9 47.1 1.0
CA A:GLN192 5.0 23.8 1.0
OE2 A:GLU146 5.0 32.7 1.0

Reference:

D.J.Pinto, R.A.Galemmo, M.L.Quan, M.J.Orwat, C.Clark, R.Li, B.Wells, F.Woerner, R.S.Alexander, K.A.Rossi, A.Smallwood, P.C.Wong, J.M.Luettgen, A.R.Rendina, R.M.Knabb, K.He, R.R.Wexler, P.Y.Lam. Discovery of Potent, Efficacious, and Orally Bioavailable Inhibitors of Blood Coagulation Factor Xa with Neutral P1 Moieties. Bioorg.Med.Chem.Lett. V. 16 5584 2006.
ISSN: ISSN 0960-894X
PubMed: 16963264
DOI: 10.1016/J.BMCL.2006.08.027
Page generated: Wed Oct 28 14:44:51 2020

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