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Chlorine in PDB 1xm4: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast, PDB code: 1xm4 was solved by G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.573, 94.317, 106.681, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.3

Other elements in 1xm4:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast (pdb code 1xm4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast, PDB code: 1xm4:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 1xm4

Go back to Chlorine Binding Sites List in 1xm4
Chlorine binding site 1 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:42.0
occ:1.00
 CL25 A:PIL1003 0.0 42.0 1.0
C24 A:PIL1003 1.7 36.6 1.0
C23 A:PIL1003 2.7 36.4 1.0
C18 A:PIL1003 2.7 40.2 1.0
N16 A:PIL1003 2.9 39.5 1.0
O17 A:PIL1003 3.0 40.3 1.0
C15 A:PIL1003 3.1 43.4 1.0
CE1 A:HIS234 3.6 21.1 1.0
NE2 A:HIS234 3.8 17.5 1.0
O A:HOH1049 3.8 41.3 1.0
CZ A:PHE414 3.9 23.1 1.0
N22 A:PIL1003 3.9 38.1 1.0
C19 A:PIL1003 3.9 39.0 1.0
CE1 A:PHE414 4.0 24.0 1.0
CD1 A:ILE410 4.1 25.1 1.0
C14 A:PIL1003 4.1 43.8 1.0
O A:HOH1011 4.3 33.7 1.0
C21 A:PIL1003 4.4 35.9 1.0
O A:HOH1007 4.4 27.8 1.0
O A:HOH1009 4.5 31.3 1.0
C1 A:PIL1003 4.8 45.8 1.0
ND1 A:HIS234 4.9 19.9 1.0
C13 A:PIL1003 4.9 42.6 1.0
O A:HOH1024 5.0 40.5 1.0

Chlorine binding site 2 out of 4 in 1xm4

Go back to Chlorine Binding Sites List in 1xm4
Chlorine binding site 2 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:46.0
occ:1.00
 CL20 A:PIL1003 0.0 46.0 1.0
C19 A:PIL1003 1.8 39.0 1.0
C18 A:PIL1003 2.7 40.2 1.0
C21 A:PIL1003 2.7 35.9 1.0
N16 A:PIL1003 3.0 39.5 1.0
O A:HOH1013 3.4 29.2 1.0
OD1 A:ASP392 3.4 15.2 1.0
CG A:ASP392 3.5 17.8 1.0
CD2 A:LEU393 3.6 20.4 1.0
CG A:LEU393 3.6 20.7 1.0
O A:ASP392 3.7 19.3 1.0
O A:HOH1029 3.7 36.5 1.0
OD2 A:ASP392 3.9 19.9 1.0
CB A:ASP392 3.9 20.8 1.0
C15 A:PIL1003 4.0 43.4 1.0
C24 A:PIL1003 4.0 36.6 1.0
N22 A:PIL1003 4.0 38.1 1.0
C A:ASP392 4.0 20.2 1.0
O A:HOH1009 4.1 31.3 1.0
SD A:MET347 4.1 35.4 1.0
CD1 A:LEU393 4.4 22.4 1.0
N A:LEU393 4.4 20.9 1.0
O17 A:PIL1003 4.5 40.3 1.0
C23 A:PIL1003 4.5 36.4 1.0
CG A:MET347 4.6 30.2 1.0
CA A:ASP392 4.6 20.2 1.0
CA A:LEU393 4.6 20.4 1.0
CB A:LEU393 4.7 21.1 1.0
C14 A:PIL1003 4.9 43.8 1.0
O A:HOH1008 5.0 34.1 1.0

Chlorine binding site 3 out of 4 in 1xm4

Go back to Chlorine Binding Sites List in 1xm4
Chlorine binding site 3 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:48.5
occ:1.00
 CL25 B:PIL1003 0.0 48.5 1.0
C24 B:PIL1003 1.8 42.3 1.0
C23 B:PIL1003 2.7 41.1 1.0
C18 B:PIL1003 2.7 44.5 1.0
O17 B:PIL1003 3.0 48.0 1.0
N16 B:PIL1003 3.0 43.6 1.0
C15 B:PIL1003 3.1 46.7 1.0
CE1 B:HIS234 3.7 21.1 1.0
O B:HOH90 3.8 45.6 1.0
N22 B:PIL1003 3.9 41.2 1.0
NE2 B:HIS234 3.9 22.4 1.0
C19 B:PIL1003 4.0 42.6 1.0
CZ B:PHE414 4.0 24.5 1.0
CE1 B:PHE414 4.1 25.3 1.0
O B:HOH18 4.2 35.0 1.0
CD1 B:ILE410 4.2 20.5 1.0
C14 B:PIL1003 4.2 48.3 1.0
O B:HOH2006 4.3 38.7 1.0
O B:HOH2008 4.4 31.1 1.0
C21 B:PIL1003 4.4 43.1 1.0
O B:HOH97 4.8 44.5 1.0
C1 B:PIL1003 4.8 47.6 1.0
ND1 B:HIS234 4.9 19.4 1.0

Chlorine binding site 4 out of 4 in 1xm4

Go back to Chlorine Binding Sites List in 1xm4
Chlorine binding site 4 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:48.2
occ:1.00
 CL20 B:PIL1003 0.0 48.2 1.0
C19 B:PIL1003 1.8 42.6 1.0
C21 B:PIL1003 2.8 43.1 1.0
C18 B:PIL1003 2.8 44.5 1.0
N16 B:PIL1003 3.1 43.6 1.0
CD2 B:LEU393 3.2 22.8 1.0
O B:HOH76 3.4 40.3 1.0
OD1 B:ASP392 3.4 15.9 1.0
CG B:ASP392 3.4 19.3 1.0
CG B:LEU393 3.5 21.8 1.0
O B:HOH17 3.5 35.7 1.0
O B:ASP392 3.6 23.6 1.0
CB B:ASP392 3.8 20.4 1.0
C B:ASP392 3.8 21.5 1.0
OD2 B:ASP392 3.9 18.3 1.0
C15 B:PIL1003 4.0 46.7 1.0
N22 B:PIL1003 4.0 41.2 1.0
C24 B:PIL1003 4.0 42.3 1.0
O B:HOH2008 4.2 31.1 1.0
N B:LEU393 4.2 22.3 1.0
SD B:MET347 4.3 32.3 1.0
CD1 B:LEU393 4.4 19.1 1.0
CA B:ASP392 4.4 21.1 1.0
CA B:LEU393 4.5 22.2 1.0
O17 B:PIL1003 4.5 48.0 1.0
C23 B:PIL1003 4.5 41.1 1.0
CB B:LEU393 4.6 21.8 1.0
CG B:MET347 4.7 27.6 1.0
C14 B:PIL1003 4.9 48.3 1.0
O B:HOH2007 5.0 32.5 1.0

Reference:

G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. Structural Basis For the Activity of Drugs That Inhibit Phosphodiesterases. Structure V. 12 2233 2004.
ISSN: ISSN 0969-2126
PubMed: 15576036
DOI: 10.1016/J.STR.2004.10.004
Page generated: Sat Jul 20 04:00:13 2024

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