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Calcium in PDB 4yt7: Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide

Enzymatic activity of Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide

All present enzymatic activity of Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide:
3.4.21.21;

Protein crystallography data

The structure of Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide, PDB code: 4yt7 was solved by A.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.36 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.400, 94.400, 108.870, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.8

Other elements in 4yt7:

The structure of Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide also contains other interesting chemical elements:

Fluorine (F) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide (pdb code 4yt7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide, PDB code: 4yt7:

Calcium binding site 1 out of 1 in 4yt7

Go back to Calcium Binding Sites List in 4yt7
Calcium binding site 1 out of 1 in the Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Viia in Complex with the Inhibitor 2-(2-{(R)-[(4- Carbamimidoylphenyl)Amino][5-Ethoxy-2-Fluoro-3-(Propan-2-Yloxy) Phenyl]Methyl}-1H-Imidazol-4-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca302

b:25.1
occ:1.00
 O H:GLU75 2.2 34.5 1.0
O H:ASP72 2.3 19.7 1.0
O H:HOH411 2.4 22.8 1.0
OE1 H:GLU70 2.4 24.5 1.0
O H:HOH495 2.4 23.0 1.0
OE1 H:GLU80 2.4 18.8 1.0
CD H:GLU70 3.3 30.0 1.0
C H:GLU75 3.4 32.6 1.0
C H:ASP72 3.4 22.5 1.0
CD H:GLU80 3.4 32.3 1.0
OE2 H:GLU70 3.6 24.9 1.0
CG H:GLU80 3.8 22.8 1.0
N H:ASP72 3.9 19.9 1.0
CA H:HIS76 4.1 25.0 1.0
N H:HIS76 4.2 26.5 1.0
CA H:ASP72 4.2 19.9 1.0
O H:HOH425 4.2 17.2 1.0
N H:LEU73 4.4 21.4 1.0
O H:HOH486 4.5 22.0 1.0
N H:ASP77 4.5 25.7 1.0
CA H:GLU75 4.5 27.9 1.0
N H:HIS71 4.5 21.1 1.0
N H:GLU75 4.5 28.0 1.0
CB H:ASP72 4.6 21.7 1.0
O H:HOH427 4.6 32.0 1.0
OE2 H:GLU80 4.6 23.1 1.0
O H:HOH437 4.6 25.2 1.0
CG H:GLU70 4.7 24.0 1.0
CA H:LEU73 4.7 21.5 1.0
CG H:GLU75 4.8 42.0 1.0
C H:HIS76 4.8 28.1 1.0
OD1 H:ASP77 4.9 29.7 1.0
C H:HIS71 4.9 22.4 1.0

Reference:

P.W.Glunz, X.Cheng, D.L.Cheney, C.A.Weigelt, A.Wei, J.M.Luettgen, P.C.Wong, R.R.Wexler, E.S.Priestley. Design and Synthesis of Potent, Selective Phenylimidazole-Based Fviia Inhibitors. Bioorg.Med.Chem.Lett. V. 25 2169 2015.
ISSN: ESSN 1464-3405
PubMed: 25881820
DOI: 10.1016/J.BMCL.2015.03.062
Page generated: Sun Jul 14 15:12:03 2024

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