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Fluorine in PDB 5a0c: Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor

Enzymatic activity of 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;

Protein crystallography data

The structure of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor, PDB code: 5a0c was solved by F.Vonnussbaum, V.M.-J.Li, S.Allerheiligen, S.Anlauf, L.Baerfacker, M.Bechem, M.Delbeck, M.F.Fitzgerald, M.Gerisch, H.Gielen-Haertwig, H.Haning, D.Karthaus, D.Lang, K.Lustig, D.Meibom, J.Mittendorf, U.Rosentreter, M.Schaefer, S.Schaefer, J.Schamberger, L.A.Telan, A.Tersteegen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.29 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 71.517, 71.517, 97.400, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 21.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor (pdb code 5a0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor, PDB code: 5a0c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5a0c

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Fluorine binding site 1 out of 6 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:16.2
occ:1.00
 F20 A:JJV1001 0.0 16.2 1.0
C18 A:JJV1001 1.3 16.2 1.0
F21 A:JJV1001 2.1 17.1 1.0
F19 A:JJV1001 2.2 16.4 1.0
C15 A:JJV1001 2.4 15.9 1.0
C17 A:JJV1001 2.8 16.1 1.0
CG2 A:VAL197 3.3 17.6 1.0
N A:SER202 3.4 15.7 1.0
O A:CYS198 3.5 13.9 1.0
C13 A:JJV1001 3.6 15.6 1.0
CB A:ALA220 3.7 15.8 1.0
C A:ASP201 3.7 16.2 1.0
CB A:VAL197 3.7 17.3 1.0
CA A:SER202 3.8 15.8 1.0
CB A:ASP201 3.9 15.8 1.0
OG A:SER202 4.0 15.6 1.0
O A:ASP201 4.1 16.3 1.0
C16 A:JJV1001 4.2 16.6 1.0
C A:CYS198 4.3 15.0 1.0
CA A:ASP201 4.3 15.7 1.0
N A:CYS198 4.3 15.8 1.0
C A:ALA220 4.5 15.0 1.0
CB A:SER202 4.6 15.5 1.0
C A:VAL197 4.6 16.3 1.0
CA A:ALA220 4.6 15.2 1.0
N A:ASP201 4.7 15.6 1.0
CG1 A:VAL197 4.7 18.4 1.0
N A:SER221 4.7 14.5 1.0
CA A:CYS198 4.8 15.5 1.0
O A:ALA220 4.8 14.9 1.0
C12 A:JJV1001 4.8 15.0 1.0
CA A:VAL197 4.8 16.5 1.0
C14 A:JJV1001 5.0 15.5 1.0

Fluorine binding site 2 out of 6 in 5a0c

Go back to Fluorine Binding Sites List in 5a0c
Fluorine binding site 2 out of 6 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:17.1
occ:1.00
 F21 A:JJV1001 0.0 17.1 1.0
C18 A:JJV1001 1.3 16.2 1.0
F20 A:JJV1001 2.1 16.2 1.0
F19 A:JJV1001 2.1 16.4 1.0
C15 A:JJV1001 2.4 15.9 1.0
C17 A:JJV1001 3.2 16.1 1.0
C13 A:JJV1001 3.3 15.6 1.0
CG2 A:VAL197 3.3 17.6 1.0
N A:PHE222 3.3 14.3 1.0
C A:SER221 3.5 14.4 1.0
N A:SER221 3.6 14.5 1.0
CA A:PHE222 3.6 14.7 1.0
C A:PHE222 3.6 15.4 1.0
O A:PHE222 3.8 16.1 1.0
C A:ALA220 3.9 15.0 1.0
O A:SER221 3.9 13.5 1.0
CB A:ALA220 4.0 15.8 1.0
CG1 A:VAL223 4.1 16.2 1.0
CA A:SER221 4.1 14.8 1.0
N A:VAL223 4.2 14.9 1.0
CA A:ALA220 4.3 15.2 1.0
O A:ALA236 4.3 15.2 1.0
CB A:VAL197 4.4 17.3 1.0
C16 A:JJV1001 4.4 16.6 1.0
C12 A:JJV1001 4.5 15.0 1.0
O A:ALA220 4.6 14.9 1.0
C14 A:JJV1001 5.0 15.5 1.0

Fluorine binding site 3 out of 6 in 5a0c

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Fluorine binding site 3 out of 6 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:16.4
occ:1.00
 F19 A:JJV1001 0.0 16.4 1.0
C18 A:JJV1001 1.3 16.2 1.0
F21 A:JJV1001 2.1 17.1 1.0
F20 A:JJV1001 2.2 16.2 1.0
C15 A:JJV1001 2.4 15.9 1.0
C13 A:JJV1001 2.9 15.6 1.0
C A:ALA220 3.1 15.0 1.0
O A:ALA220 3.2 14.9 1.0
OG A:SER202 3.2 15.6 1.0
O A:SER221 3.2 13.5 1.0
C A:SER221 3.2 14.4 1.0
N A:SER221 3.3 14.5 1.0
CA A:SER202 3.3 15.8 1.0
CA A:SER221 3.6 14.8 1.0
CE1 A:HIS57 3.6 16.0 1.0
C17 A:JJV1001 3.7 16.1 1.0
CB A:ALA220 3.7 15.8 1.0
CB A:SER202 3.7 15.5 1.0
N A:SER202 3.8 15.7 1.0
N A:PHE222 3.8 14.3 1.0
NE2 A:HIS57 3.9 15.8 1.0
CA A:ALA220 4.0 15.2 1.0
C12 A:JJV1001 4.3 15.0 1.0
CA A:PHE222 4.4 14.7 1.0
C A:ASP201 4.5 16.2 1.0
C A:SER202 4.5 15.3 1.0
N A:GLY203 4.6 15.1 1.0
O A:ASP201 4.7 16.3 1.0
C16 A:JJV1001 4.8 16.6 1.0
ND1 A:HIS57 4.9 16.6 1.0
CG2 A:VAL197 4.9 17.6 1.0
C A:PHE222 5.0 15.4 1.0

Fluorine binding site 4 out of 6 in 5a0c

Go back to Fluorine Binding Sites List in 5a0c
Fluorine binding site 4 out of 6 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 4 of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:15.5
occ:1.00
 F20 B:JJV1001 0.0 15.5 1.0
C18 B:JJV1001 1.4 15.6 1.0
F21 B:JJV1001 2.1 16.2 1.0
F19 B:JJV1001 2.2 15.9 1.0
C15 B:JJV1001 2.4 15.2 1.0
C17 B:JJV1001 2.9 15.4 1.0
N B:SER202 3.2 14.6 1.0
CG2 B:VAL197 3.4 18.0 1.0
O B:CYS198 3.5 13.9 1.0
CB B:ALA220 3.5 15.6 1.0
C B:ASP201 3.6 15.3 1.0
CA B:SER202 3.6 14.9 1.0
C13 B:JJV1001 3.7 14.7 1.0
CB B:ASP201 3.7 14.6 1.0
CB B:VAL197 3.8 17.7 1.0
OG B:SER202 4.0 14.1 1.0
O B:ASP201 4.0 14.9 1.0
CA B:ASP201 4.2 14.6 1.0
C16 B:JJV1001 4.2 15.4 1.0
N B:CYS198 4.3 16.1 1.0
C B:CYS198 4.3 15.0 1.0
CB B:SER202 4.4 14.5 1.0
C B:ALA220 4.4 15.3 1.0
CA B:ALA220 4.5 15.4 1.0
N B:ASP201 4.5 15.0 1.0
C B:VAL197 4.6 16.2 1.0
O B:ALA220 4.7 15.8 1.0
CG1 B:VAL197 4.7 18.7 1.0
N B:SER221 4.7 15.2 1.0
CA B:CYS198 4.8 16.0 1.0
CA B:VAL197 4.8 16.4 1.0
C12 B:JJV1001 4.8 14.1 1.0
C B:SER202 4.9 14.5 1.0

Fluorine binding site 5 out of 6 in 5a0c

Go back to Fluorine Binding Sites List in 5a0c
Fluorine binding site 5 out of 6 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 5 of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:16.2
occ:1.00
 F21 B:JJV1001 0.0 16.2 1.0
C18 B:JJV1001 1.3 15.6 1.0
F20 B:JJV1001 2.1 15.5 1.0
F19 B:JJV1001 2.1 15.9 1.0
C15 B:JJV1001 2.3 15.2 1.0
C17 B:JJV1001 3.1 15.4 1.0
CG2 B:VAL197 3.2 18.0 1.0
C13 B:JJV1001 3.2 14.7 1.0
N B:PHE222 3.4 14.7 1.0
C B:SER221 3.6 14.6 1.0
N B:SER221 3.6 15.2 1.0
CA B:PHE222 3.7 14.8 1.0
C B:PHE222 3.7 15.8 1.0
CB B:ALA220 3.9 15.6 1.0
C B:ALA220 3.9 15.3 1.0
O B:PHE222 3.9 16.1 1.0
CG1 B:VAL223 4.0 16.2 1.0
O B:SER221 4.0 14.6 1.0
CA B:SER221 4.1 14.7 1.0
N B:VAL223 4.3 15.9 1.0
CA B:ALA220 4.3 15.4 1.0
CB B:VAL197 4.3 17.7 1.0
C16 B:JJV1001 4.3 15.4 1.0
O B:ALA236 4.4 15.3 1.0
C12 B:JJV1001 4.5 14.1 1.0
O B:ALA220 4.6 15.8 1.0
C14 B:JJV1001 4.9 14.6 1.0
OG B:SER202 5.0 14.1 1.0

Fluorine binding site 6 out of 6 in 5a0c

Go back to Fluorine Binding Sites List in 5a0c
Fluorine binding site 6 out of 6 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 6 of Crystal Structure of Human Neutrophil Elastase in Complex with A Dihydropyrimidone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:15.9
occ:1.00
 F19 B:JJV1001 0.0 15.9 1.0
C18 B:JJV1001 1.3 15.6 1.0
F21 B:JJV1001 2.1 16.2 1.0
F20 B:JJV1001 2.2 15.5 1.0
C15 B:JJV1001 2.4 15.2 1.0
C13 B:JJV1001 2.9 14.7 1.0
C B:ALA220 3.1 15.3 1.0
O B:ALA220 3.2 15.8 1.0
OG B:SER202 3.2 14.1 1.0
C B:SER221 3.2 14.6 1.0
N B:SER221 3.2 15.2 1.0
O B:SER221 3.2 14.6 1.0
CA B:SER202 3.3 14.9 1.0
CA B:SER221 3.5 14.7 1.0
CB B:SER202 3.6 14.5 1.0
CE1 B:HIS57 3.7 14.9 1.0
CB B:ALA220 3.7 15.6 1.0
C17 B:JJV1001 3.7 15.4 1.0
N B:SER202 3.8 14.6 1.0
N B:PHE222 3.8 14.7 1.0
NE2 B:HIS57 3.9 14.7 1.0
CA B:ALA220 3.9 15.4 1.0
C12 B:JJV1001 4.3 14.1 1.0
CA B:PHE222 4.4 14.8 1.0
C B:SER202 4.5 14.5 1.0
N B:GLY203 4.5 14.6 1.0
C B:ASP201 4.6 15.3 1.0
O B:ASP201 4.8 14.9 1.0
C16 B:JJV1001 4.8 15.4 1.0
ND1 B:HIS57 4.9 15.3 1.0
CG2 B:VAL197 4.9 18.0 1.0

Reference:

F.Von Nussbaum, V.M.Li, S.Allerheiligen, S.Anlauf, L.Barfacker, M.Bechem, M.Delbeck, M.F.Fitzgerald, M.Gerisch, H.Gielen-Haertwig, H.Haning, D.Karthaus, D.Lang, K.Lustig, D.Meibom, J.Mittendorf, U.Rosentreter, M.Schafer, S.Schafer, J.Schamberger, L.A.Telan, A.Tersteegen. Freezing the Bioactive Conformation to Boost Potency: the Identification of Bay 85-8501, A Selective and Potent Inhibitor of Human Neutrophil Elastase For Pulmonary Diseases. Chemmedchem V. 10 1163 2015.
ISSN: ESSN 1860-7187
PubMed: 26083237
DOI: 10.1002/CMDC.201500131
Page generated: Thu Aug 1 07:34:19 2024

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