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Fluorine in PDB 1z6e: Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389):
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)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389), PDB code: 1z6e 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) 28.18 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.100, 71.700, 78.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 26

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)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389) (pdb code 1z6e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389), PDB code: 1z6e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1z6e

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Fluorine binding site 1 out of 4 in the Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)


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)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:36.5
occ:1.00
 F A:IK8711 0.0 36.5 1.0
C10 A:IK8711 1.3 35.1 1.0
F2 A:IK8711 2.1 36.4 1.0
F1 A:IK8711 2.1 35.7 1.0
C7 A:IK8711 2.3 33.8 1.0
C8 A:IK8711 3.1 31.8 1.0
N3 A:IK8711 3.4 31.8 1.0
CG A:GLU146 3.5 36.6 1.0
OE2 A:GLU146 3.9 38.2 1.0
CD A:GLU146 4.0 37.2 1.0
CA A:GLY218 4.2 23.7 1.0
O A:GLU146 4.3 35.9 1.0
C9 A:IK8711 4.3 31.9 1.0
N2 A:IK8711 4.4 31.2 1.0
SG A:CYS220 4.6 27.8 1.0
CB A:GLU146 4.8 35.4 1.0
N A:GLY218 4.8 23.5 1.0
C A:GLY218 4.9 23.8 1.0
OE1 A:GLU146 5.0 35.2 1.0

Fluorine binding site 2 out of 4 in 1z6e

Go back to Fluorine Binding Sites List in 1z6e
Fluorine binding site 2 out of 4 in the Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)


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)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:35.7
occ:1.00
 F1 A:IK8711 0.0 35.7 1.0
C10 A:IK8711 1.3 35.1 1.0
F A:IK8711 2.1 36.5 1.0
F2 A:IK8711 2.2 36.4 1.0
C7 A:IK8711 2.3 33.8 1.0
C8 A:IK8711 3.0 31.8 1.0
N3 A:IK8711 3.4 31.8 1.0
OE1 A:GLN192 3.8 41.1 1.0
CB A:GLN192 4.1 25.2 1.0
CG A:GLN192 4.2 30.7 1.0
C9 A:IK8711 4.3 31.9 1.0
N2 A:IK8711 4.4 31.2 1.0
CD A:GLN192 4.5 37.6 1.0
NE A:ARG143 4.6 36.9 1.0
O A:GLU146 4.8 35.9 1.0
CD A:ARG143 5.0 33.3 1.0

Fluorine binding site 3 out of 4 in 1z6e

Go back to Fluorine Binding Sites List in 1z6e
Fluorine binding site 3 out of 4 in the Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)


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)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:36.4
occ:1.00
 F2 A:IK8711 0.0 36.4 1.0
C10 A:IK8711 1.3 35.1 1.0
F A:IK8711 2.1 36.5 1.0
F1 A:IK8711 2.2 35.7 1.0
C7 A:IK8711 2.3 33.8 1.0
N3 A:IK8711 2.8 31.8 1.0
O A:GLU146 3.5 35.9 1.0
CB A:GLN192 3.6 25.2 1.0
CD A:ARG143 3.7 33.3 1.0
C8 A:IK8711 3.7 31.8 1.0
NE A:ARG143 3.8 36.9 1.0
SG A:CYS220 3.9 27.8 1.0
CG A:GLU146 3.9 36.6 1.0
SG A:CYS191 3.9 23.2 1.0
N2 A:IK8711 4.1 31.2 1.0
C A:GLU146 4.3 36.0 1.0
CA A:GLU146 4.3 35.1 1.0
N A:GLN192 4.4 21.2 1.0
CG A:GLN192 4.4 30.7 1.0
C9 A:IK8711 4.6 31.9 1.0
CA A:GLN192 4.6 21.9 1.0
OE1 A:GLN192 4.7 41.1 1.0
CB A:GLU146 4.7 35.4 1.0
CZ A:ARG143 4.8 40.6 1.0
CD A:GLU146 5.0 37.2 1.0

Fluorine binding site 4 out of 4 in 1z6e

Go back to Fluorine Binding Sites List in 1z6e
Fluorine binding site 4 out of 4 in the Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Factor Xa in Complex with the Inhibitor 1-(3'-Amino-1,2-Benzisoxazol- 5'-Yl)-N-(4-(2'-((Dimethylamino)Methyl)-1H-Imidazol-1-Yl)-2- Fluorophenyl)-3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (Razaxaban; DPC906; Bms-561389) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F711

b:35.1
occ:1.00
 F3 A:IK8711 0.0 35.1 1.0
C15 A:IK8711 1.3 33.0 1.0
C16 A:IK8711 2.4 34.1 1.0
C14 A:IK8711 2.4 32.7 1.0
N4 A:IK8711 2.8 31.7 1.0
O1 A:IK8711 2.9 29.8 1.0
C13 A:IK8711 3.0 32.2 1.0
O A:HOH784 3.1 27.8 1.0
O A:HOH758 3.1 25.9 1.0
OH A:TYR99 3.2 25.1 1.0
CZ A:TYR99 3.4 24.5 1.0
CE2 A:TYR99 3.5 23.9 1.0
C17 A:IK8711 3.7 35.1 1.0
C19 A:IK8711 3.7 32.6 1.0
CB A:TRP215 3.9 18.1 1.0
C18 A:IK8711 4.2 33.5 1.0
CE1 A:TYR99 4.2 25.9 1.0
C9 A:IK8711 4.2 31.9 1.0
CD2 A:TYR99 4.4 24.1 1.0
N5 A:IK8711 4.8 36.7 1.0
CA A:TRP215 4.8 18.2 1.0
CG A:TRP215 4.9 18.6 1.0
CD1 A:TYR99 5.0 25.2 1.0

Reference:

M.L.Quan, P.Y.S.Lam, Q.Han, D.J.P.Pinto, M.Y.He, R.Li, C.D.Ellis, C.G.Clark, C.A.Teleha, J.-H.Sun, R.S.Alexander, S.Bai, J.M.Luettgen, R.M.Knabb, P.C.Wong, R.R.Wexler. Discovery of 1-(3'-Aminobenzisoxazol-5'-Yl)-3-Trifluoromethyl-N-[2- Fluoro-4-[(2'-Dimethylaminomethyl)Imidazol-1-Yl]Phenyl]-1H- Pyrazole-5-Carboxyamide Hydrochloride (Razaxaban), A Highly Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor. J.Med.Chem. V. 48 1729 2005.
ISSN: ISSN 0022-2623
PubMed: 15771420
DOI: 10.1021/JM0497949
Page generated: Mon Jul 14 12:29:30 2025

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