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Fluorine in PDB 5pax: Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea

Enzymatic activity of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea

All present enzymatic activity of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea, PDB code: 5pax was solved by M.Stihle, A.Mayweg, S.Roever, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.36 / 1.36
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.240, 95.240, 116.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.2

Other elements in 5pax:

The structure of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea (pdb code 5pax). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea, PDB code: 5pax:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5pax

Go back to Fluorine Binding Sites List in 5pax
Fluorine binding site 1 out of 2 in the Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F505

b:39.5
occ:1.00
F26 C:7ZP505 0.0 39.5 1.0
C16 C:7ZP505 1.4 36.9 1.0
C33 C:7ZP505 2.4 38.0 1.0
C9 C:7ZP505 2.4 36.3 1.0
N13 C:7ZP505 2.8 32.4 1.0
O19 C:7ZP505 3.0 32.4 1.0
C10 C:7ZP505 3.1 32.8 1.0
CH2 C:TRP424 3.3 28.3 1.0
CZ3 C:TRP424 3.5 28.3 1.0
C31 C:7ZP505 3.6 38.2 1.0
C17 C:7ZP505 3.6 37.2 1.0
C32 C:7ZP505 4.1 38.1 1.0
N15 C:7ZP505 4.2 29.6 1.0
O C:HOH672 4.2 49.1 1.0
CZ2 C:TRP424 4.5 28.0 1.0
F27 C:7ZP505 4.8 37.5 1.0
CA C:GLY297 4.8 26.5 1.0
CE3 C:TRP424 4.8 28.8 1.0
OD2 C:ASP256 5.0 20.8 1.0

Fluorine binding site 2 out of 2 in 5pax

Go back to Fluorine Binding Sites List in 5pax
Fluorine binding site 2 out of 2 in the Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Factor Viia in Complex with 1-(2,6- Difluorophenyl)-3-[[3-[5-Hydroxy-4-(1H-Pyrrolo[3,2-C]Pyridin-2-Yl) Pyrazol-1-Yl]Phenyl]Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F505

b:37.5
occ:1.00
F27 C:7ZP505 0.0 37.5 1.0
C17 C:7ZP505 1.3 37.2 1.0
C32 C:7ZP505 2.4 38.1 1.0
C9 C:7ZP505 2.4 36.3 1.0
N13 C:7ZP505 2.8 32.4 1.0
OD2 C:ASP256 3.0 20.8 1.0
CB C:ASP256 3.3 18.9 1.0
CG C:ASP256 3.3 18.8 1.0
N C:GLY297 3.4 24.9 1.0
CA C:GLY297 3.6 26.5 1.0
C31 C:7ZP505 3.6 38.2 1.0
C16 C:7ZP505 3.6 36.9 1.0
C10 C:7ZP505 3.7 32.8 1.0
C C:PRO296 3.8 23.5 1.0
CB C:PRO296 3.8 22.0 1.0
CE C:LYS257 3.9 34.5 1.0
NZ C:LYS257 4.0 34.4 1.0
C33 C:7ZP505 4.1 38.0 1.0
CA C:PRO296 4.2 21.8 1.0
OD1 C:ASP256 4.2 18.3 1.0
O19 C:7ZP505 4.2 32.4 1.0
O C:PRO296 4.3 24.2 1.0
CA C:ASP256 4.5 19.3 1.0
N15 C:7ZP505 4.6 29.6 1.0
CD C:LYS257 4.6 32.6 1.0
O C:ASP256 4.7 22.9 1.0
F26 C:7ZP505 4.8 39.5 1.0
C C:ASP256 4.8 21.4 1.0
O C:HOH757 4.8 60.3 1.0

Reference:

A.Mayweg, S.Roever, M.G.Rudolph. Crystal Structure of A Factor Viia Complex To Be Published.
Page generated: Tue Jul 15 06:02:00 2025

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