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Fluorine in PDB 1x7a: Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide

Enzymatic activity of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide

All present enzymatic activity of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide:
3.4.21.22;

Protein crystallography data

The structure of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide, PDB code: 1x7a was solved by R.S.Alexander, A.M.Smallwood, J.M.Smallheer, J.Wang, S.Wang, S.Nakajima, K.A.Rossi, F.Barbera, D.Burdick, J.M.Luettgen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 129.000, 129.000, 71.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (pdb code 1x7a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide, PDB code: 1x7a:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1x7a

Go back to Fluorine Binding Sites List in 1x7a
Fluorine binding site 1 out of 4 in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F298

b:42.2
occ:1.00
 F1 C:187298 0.0 42.2 1.0
C11 C:187298 1.3 41.5 1.0
F2 C:187298 2.0 43.1 1.0
F3 C:187298 2.1 42.1 1.0
C10 C:187298 2.4 41.3 1.0
N6 C:187298 2.9 40.0 1.0
NH2 C:ARG143 2.9 48.9 1.0
SG C:CYS191 3.6 41.9 1.0
SG C:CYS220 3.7 38.0 1.0
C12 C:187298 3.8 36.5 1.0
N C:ARG148 4.0 38.4 1.0
CB C:GLN192 4.0 33.0 1.0
CZ C:ARG143 4.1 45.2 1.0
N1 C:187298 4.2 38.4 1.0
CA C:ARG148 4.2 40.3 1.0
NE2 C:GLN192 4.3 39.8 1.0
CG C:ARG143 4.4 32.0 1.0
OD1 C:ASN147 4.5 40.8 1.0
C13 C:187298 4.6 34.6 1.0
CB C:ARG148 4.6 37.1 1.0
CB C:CYS220 4.7 38.3 1.0
NH1 C:ARG143 4.7 42.3 1.0
N C:GLN192 4.8 36.4 1.0
CD C:GLN192 4.8 40.2 1.0
CG C:GLN192 4.9 37.9 1.0
NE C:ARG143 4.9 40.0 1.0
C C:ASN147 5.0 38.4 1.0

Fluorine binding site 2 out of 4 in 1x7a

Go back to Fluorine Binding Sites List in 1x7a
Fluorine binding site 2 out of 4 in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F298

b:42.1
occ:1.00
 F3 C:187298 0.0 42.1 1.0
C11 C:187298 1.3 41.5 1.0
F2 C:187298 2.0 43.1 1.0
F1 C:187298 2.1 42.2 1.0
C10 C:187298 2.3 41.3 1.0
C12 C:187298 3.1 36.5 1.0
N6 C:187298 3.5 40.0 1.0
NH2 C:ARG143 4.2 48.9 1.0
C13 C:187298 4.3 34.6 1.0
CG C:GLU219 4.5 40.8 1.0
N1 C:187298 4.5 38.4 1.0
CB C:ARG148 4.6 37.1 1.0
N C:ARG148 4.7 38.4 1.0
CA C:GLU219 4.8 34.0 1.0
CA C:ARG148 4.8 40.3 1.0
CG C:ARG148 4.9 33.8 0.0
SG C:CYS220 4.9 38.0 1.0
NE2 C:GLN192 4.9 39.8 1.0
OD1 C:ASN147 4.9 40.8 1.0
ND2 C:ASN147 5.0 40.4 1.0

Fluorine binding site 3 out of 4 in 1x7a

Go back to Fluorine Binding Sites List in 1x7a
Fluorine binding site 3 out of 4 in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F298

b:43.1
occ:1.00
 F2 C:187298 0.0 43.1 1.0
C11 C:187298 1.2 41.5 1.0
F1 C:187298 2.0 42.2 1.0
F3 C:187298 2.0 42.1 1.0
C10 C:187298 2.2 41.3 1.0
NE2 C:GLN192 2.9 39.8 1.0
C12 C:187298 3.1 36.5 1.0
N6 C:187298 3.2 40.0 1.0
NH2 C:ARG143 3.2 48.9 1.0
CD C:GLN192 3.8 40.2 1.0
CB C:GLN192 3.8 33.0 1.0
CZ C:ARG143 4.0 45.2 1.0
CG C:GLN192 4.1 37.9 1.0
NH1 C:ARG143 4.1 42.3 1.0
C13 C:187298 4.3 34.6 1.0
N1 C:187298 4.3 38.4 1.0
OE1 C:GLN192 4.7 41.4 1.0

Fluorine binding site 4 out of 4 in 1x7a

Go back to Fluorine Binding Sites List in 1x7a
Fluorine binding site 4 out of 4 in the Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Porcine Factor Ixa Complexed to 1-{3-[Amino(Imino) Methyl]Phenyl}-N-[4-(1H-Benzimidazol-1-Yl)-2-Fluorophenyl]- 3-(Trifluoromethyl)-1H-Pyrazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F298

b:22.4
occ:1.00
 F4 C:187298 0.0 22.4 1.0
C44 C:187298 1.3 26.1 1.0
C7 C:187298 2.3 25.4 1.0
C14 C:187298 2.4 25.2 1.0
N5 C:187298 2.6 27.5 1.0
O C:GLY216 3.0 24.9 1.0
CA C:GLU217 3.1 30.5 1.0
N C:GLU219 3.3 32.6 1.0
N C:GLU217 3.5 26.5 1.0
C C:GLY216 3.5 23.9 1.0
C8 C:187298 3.6 29.8 1.0
C22 C:187298 3.6 25.6 1.0
C C:GLU217 3.6 31.8 1.0
C16 C:187298 3.7 28.8 1.0
C18 C:187298 4.2 27.1 1.0
CB C:GLU217 4.2 27.7 1.0
O3 C:187298 4.2 30.6 1.0
C13 C:187298 4.4 34.6 1.0
CA C:GLU219 4.5 34.0 1.0
CG C:GLU217 4.6 31.5 1.0
C12 C:187298 4.7 36.5 1.0
N7 C:187298 4.8 32.3 1.0
CA C:GLY216 4.8 22.8 1.0
O C:GLU217 4.8 35.5 1.0
N C:GLY216 4.9 21.4 1.0
CZ C:PHE174 5.0 32.1 1.0

Reference:

J.M.Smallheer, R.S.Alexander, J.Wang, S.Wang, S.Nakajima, K.A.Rossi, A.Smallwood, F.Barbera, D.Burdick, J.M.Luettgen, R.M.Knabb, R.R.Wexler, P.K.Jadhav. Sar and Factor Ixa Crystal Structure of A Dual Inhibitor of Factors Ixa and Xa Bioorg.Med.Chem.Lett. V. 14 5263 2004.
ISSN: ISSN 0960-894X
PubMed: 15454208
DOI: 10.1016/J.BMCL.2004.08.034
Page generated: Wed Jul 31 13:16:23 2024

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