Atomistry » Fluorine » PDB 1xz3-1zzr » 1z6e
Atomistry »
  Fluorine »
    PDB 1xz3-1zzr »
      1z6e »

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

Go back to Fluorine Binding Sites List in 1z6e
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy