Fluorine in PDB 5a8y: Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor

All present enzymatic activity of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor:
3.4.21.37;

The structure of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor, PDB code: 5a8y was solved by F.Vonnussbaum, V.M.Li, D.Meibom, S.Anlauf, M.Bechem, M.Delbeck, M.Gerisch, A.Harrenga, D.Karthaus, D.Lang, K.Lustig, J.Mittendorf, M.Schaefer, S.Schaefer, J.Schamberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.51 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	73.025, 73.025, 69.842, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 22.1

The binding sites of Fluorine atom in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor (pdb code 5a8y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor, PDB code: 5a8y:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor


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 Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:12.6 occ:1.00 F29 A:VBM1001 0.0 12.6 1.0 C27 A:VBM1001 1.3 12.9 1.0 F28 A:VBM1001 2.1 11.2 1.0 F30 A:VBM1001 2.1 11.9 1.0 C25 A:VBM1001 2.3 11.2 1.0 C24 A:VBM1001 3.0 11.8 1.0 C26 A:VBM1001 3.2 12.4 1.0 N A:PHE215 3.3 9.8 1.0 CG2 A:VAL190 3.4 10.0 1.0 C A:SER214 3.6 9.2 1.0 N A:SER214 3.6 10.1 1.0 CG1 A:VAL216 3.6 12.4 1.0 CA A:PHE215 3.7 10.0 1.0 C A:PHE215 3.7 11.8 1.0 O A:PHE215 3.9 11.0 1.0 CB A:ALA213 3.9 8.2 1.0 O A:SER214 4.0 8.9 1.0 C A:ALA213 4.0 10.1 1.0 CA A:SER214 4.1 9.1 1.0 N A:VAL216 4.2 12.4 1.0 C23 A:VBM1001 4.3 12.4 1.0 CA A:ALA213 4.4 9.6 1.0 O A:ALA227 4.4 11.6 1.0 C21 A:VBM1001 4.5 14.6 1.0 CB A:VAL190 4.5 9.9 1.0 O A:ALA213 4.5 9.3 1.0 C22 A:VBM1001 4.8 14.7 1.0 CB A:VAL216 4.9 14.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor


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 Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:11.9 occ:1.00 F30 A:VBM1001 0.0 11.9 1.0 C27 A:VBM1001 1.3 12.9 1.0 F29 A:VBM1001 2.1 12.6 1.0 F28 A:VBM1001 2.2 11.2 1.0 C25 A:VBM1001 2.4 11.2 1.0 C26 A:VBM1001 2.8 12.4 1.0 O A:SER214 3.1 8.9 1.0 C A:SER214 3.2 9.2 1.0 O A:ALA213 3.2 9.3 1.0 C A:ALA213 3.2 10.1 1.0 N A:SER214 3.2 10.1 1.0 CA A:SER195 3.3 8.4 1.0 OG A:SER195 3.3 12.0 1.0 CA A:SER214 3.5 9.1 1.0 C24 A:VBM1001 3.6 11.8 1.0 CB A:ALA213 3.7 8.2 1.0 N A:PHE215 3.7 9.8 1.0 CE1 A:HIS57 3.7 12.4 1.0 CB A:SER195 3.8 9.5 1.0 N A:SER195 3.8 8.1 1.0 NE2 A:HIS57 4.0 10.8 1.0 CA A:ALA213 4.1 9.6 1.0 C21 A:VBM1001 4.2 14.6 1.0 CA A:PHE215 4.3 10.0 1.0 C A:SER195 4.5 8.6 1.0 C A:ASP194 4.6 6.9 1.0 N A:GLY196 4.6 9.0 1.0 C23 A:VBM1001 4.8 12.4 1.0 O A:ASP194 4.8 7.4 1.0 ND1 A:HIS57 5.0 10.8 1.0 N4 A:VBM1001 5.0 13.2 1.0 CB A:SER214 5.0 10.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:11.2 occ:1.00 F28 A:VBM1001 0.0 11.2 1.0 C27 A:VBM1001 1.3 12.9 1.0 F29 A:VBM1001 2.1 12.6 1.0 F30 A:VBM1001 2.2 11.9 1.0 C25 A:VBM1001 2.3 11.2 1.0 C24 A:VBM1001 2.8 11.8 1.0 N A:SER195 3.2 8.1 1.0 O A:CYS191 3.4 9.9 1.0 C26 A:VBM1001 3.5 12.4 1.0 CA A:SER195 3.6 8.4 1.0 CG2 A:VAL190 3.6 10.0 1.0 C A:ASP194 3.6 6.9 1.0 CB A:ALA213 3.6 8.2 1.0 CB A:ASP194 3.9 6.6 1.0 OG A:SER195 3.9 12.0 1.0 CB A:VAL190 4.0 9.9 1.0 O A:ASP194 4.1 7.4 1.0 C23 A:VBM1001 4.1 12.4 1.0 C A:CYS191 4.2 11.0 1.0 CA A:ASP194 4.2 7.8 1.0 N A:CYS191 4.3 9.8 1.0 CB A:SER195 4.4 9.5 1.0 C A:ALA213 4.5 10.1 1.0 N A:ASP194 4.5 7.1 1.0 CA A:ALA213 4.6 9.6 1.0 O A:ALA213 4.7 9.3 1.0 N A:SER214 4.7 10.1 1.0 CA A:CYS191 4.7 10.5 1.0 CG1 A:VAL216 4.7 12.4 1.0 C21 A:VBM1001 4.7 14.6 1.0 C A:VAL190 4.8 8.8 1.0 C A:SER195 4.9 8.6 1.0 C22 A:VBM1001 4.9 14.7 1.0

F.Von Nussbaum, V.M.Li, D.Meibom, S.Anlauf, M.Bechem, M.Delbeck, M.Gerisch, A.Harrenga, D.Karthaus, D.Lang, K.Lustig, J.Mittendorf, M.Schafer, S.Schafer, J.Schamberger. Potent and Selective Human Neutrophil Elastase Inhibitors with Novel Equatorial Ring Topology: in Vivo Efficacy of the Polar Pyrimidopyridazine Bay-8040 in A Pulmonary Arterial Hypertension Rat Model. Chemmedchem V. 11 199 2016.
ISSN: ISSN 1860-7179
PubMed: 26333652
DOI: 10.1002/CMDC.201500269