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Fluorine in PDB 2aei: Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid

Enzymatic activity of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid

All present enzymatic activity of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid, PDB code: 2aei was solved by M.Adler, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.215, 80.496, 125.936, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 29.7

Other elements in 2aei:

The structure of Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid also contains other interesting chemical elements:

Arsenic (As) 1 atom
Calcium (Ca) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid (pdb code 2aei). 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 A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid, PDB code: 2aei:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 2aei

Go back to Fluorine Binding Sites List in 2aei
Fluorine binding site 1 out of 2 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


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 A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F500

b:48.6
occ:1.00
 F7 H:03R500 0.0 48.6 1.0
C3 H:03R500 1.3 36.6 1.0
C1 H:03R500 2.3 32.4 1.0
C6 H:03R500 2.3 37.3 1.0
O4 H:03R500 2.6 26.1 1.0
N11 H:03R500 2.7 33.6 1.0
C9 H:03R500 3.6 38.7 1.0
N2 H:03R500 3.6 36.2 1.0
C16 H:03R500 3.9 23.8 1.0
C8 H:03R500 4.0 23.5 1.0
C5 H:03R500 4.1 38.8 1.0
O26 H:03R500 4.4 18.6 1.0
C23 H:03R500 4.6 17.3 1.0
C13 H:03R500 4.6 17.7 1.0
F14 H:03R500 4.7 45.3 1.0
CD2 H:HIS57 4.8 10.2 1.0

Fluorine binding site 2 out of 2 in 2aei

Go back to Fluorine Binding Sites List in 2aei
Fluorine binding site 2 out of 2 in the Crystal Structure of A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid


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 A Ternary Complex of Factor Viia/Tissue Factor and 2-[[6-[3-(Aminoiminomethyl)Phenoxy]-3,5-Difluro-4-[(1-Methyl-3- Phenylpropyl)Amino]-2-Pyridinyl]Oxy]-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F500

b:45.3
occ:1.00
 F14 H:03R500 0.0 45.3 1.0
C9 H:03R500 1.3 38.7 1.0
C5 H:03R500 2.3 38.8 1.0
C6 H:03R500 2.3 37.3 1.0
O10 H:03R500 2.5 42.0 1.0
N11 H:03R500 2.8 33.6 1.0
C23 H:03R500 2.8 17.3 1.0
CB H:TRP215 2.9 4.9 1.0
C35 H:03R500 3.0 36.6 1.0
C16 H:03R500 3.0 23.8 1.0
C22 H:03R500 3.4 23.7 1.0
CA H:TRP215 3.5 2.8 1.0
N2 H:03R500 3.6 36.2 1.0
C3 H:03R500 3.6 36.6 1.0
C32 H:03R500 3.6 34.3 1.0
C37 H:03R500 3.6 39.6 1.0
C15 H:03R500 3.7 39.0 1.0
O H:SER214 3.7 2.5 1.0
C29 H:03R500 3.9 30.3 1.0
C1 H:03R500 4.1 32.4 1.0
CG H:TRP215 4.1 2.4 1.0
C20 H:03R500 4.4 40.7 1.0
N H:GLY216 4.4 7.5 1.0
N H:TRP215 4.5 5.5 1.0
C H:SER214 4.5 3.4 1.0
C36 H:03R500 4.5 34.3 1.0
C39 H:03R500 4.5 39.7 1.0
C H:TRP215 4.5 6.5 1.0
CE1 H:HIS57 4.7 13.3 1.0
F7 H:03R500 4.7 48.6 1.0
C21 H:03R500 4.7 35.4 1.0
O H:GLY216 4.9 11.1 1.0
ND1 H:HIS57 4.9 14.0 1.0
C38 H:03R500 4.9 37.9 1.0
CD2 H:TRP215 5.0 6.4 1.0

Reference:

J.T.Kohrt, K.J.Filipski, W.L.Cody, C.Cai, D.A.Dudley, C.A.Van Huis, J.A.Willardsen, S.T.Rapundalo, K.Saiya-Cork, R.J.Leadley, L.Narasimhan, E.Zhang, M.Whitlow, M.Adler, K.Mclean, Y.L.Chou, C.Mcknight, D.O.Arnaiz, K.J.Shaw, D.R.Light, J.J.Edmunds. The Discovery of Fluoropyridine-Based Inhibitors of the Factor Viia/Tf Complex. Bioorg.Med.Chem.Lett. V. 15 4752 2005.
ISSN: ISSN 0960-894X
PubMed: 16125385
DOI: 10.1016/J.BMCL.2005.07.059
Page generated: Sun Dec 13 11:34:44 2020

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