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Chlorine in PDB 1y2h: Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2h was solved by G.L.Card, L.Blasdel, B.P.England, C.Zhang, Y.Suzuki, S.Gillette, D.Fong, 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.541, 94.178, 106.819, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 29.9

Other elements in 1y2h:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester 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 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2h:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 1y2h

Go back to Chlorine Binding Sites List in 1y2h
Chlorine binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester


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 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:0.2
occ:1.00
CL4 A:6DE101 0.0 0.2 1.0
C3 A:6DE101 1.7 0.9 1.0
C2 A:6DE101 2.7 0.8 1.0
C5 A:6DE101 2.7 0.9 1.0
N1 A:6DE101 2.9 0.4 1.0
CD2 A:LEU393 3.1 36.1 1.0
C18 A:6DE101 3.5 0.3 1.0
N9 A:6DE101 3.5 0.3 1.0
CZ A:PHE446 3.6 30.9 1.0
CE1 A:PHE446 3.9 30.1 1.0
SD A:MET347 3.9 42.7 1.0
C19 A:6DE101 4.0 0.3 1.0
C8 A:6DE101 4.0 0.0 1.0
C6 A:6DE101 4.0 0.0 1.0
CE A:MET347 4.1 40.8 1.0
CG A:MET347 4.2 39.5 1.0
C10 A:6DE101 4.2 0.2 1.0
C12 A:6DE101 4.2 0.2 1.0
C7 A:6DE101 4.5 0.2 1.0
CG A:LEU393 4.5 34.6 1.0
CE2 A:PHE446 4.7 31.5 1.0
CD1 A:LEU393 4.8 35.2 1.0

Chlorine binding site 2 out of 2 in 1y2h

Go back to Chlorine Binding Sites List in 1y2h
Chlorine binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester


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 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:0.1
occ:1.00
CL4 B:6DE102 0.0 0.1 1.0
C3 B:6DE102 1.7 0.6 1.0
C2 B:6DE102 2.7 0.6 1.0
C5 B:6DE102 2.7 0.6 1.0
N1 B:6DE102 3.0 0.3 1.0
CD2 B:LEU393 3.0 37.8 1.0
C18 B:6DE102 3.4 0.4 1.0
O B:HOH12 3.5 56.5 1.0
C19 B:6DE102 3.7 0.4 1.0
N9 B:6DE102 3.8 0.1 1.0
CZ B:PHE446 3.9 31.1 1.0
SD B:MET347 4.0 42.5 1.0
C8 B:6DE102 4.0 0.9 1.0
C6 B:6DE102 4.0 0.8 1.0
C12 B:6DE102 4.3 0.1 1.0
O B:HOH2008 4.3 68.9 1.0
CE1 B:PHE446 4.4 32.1 1.0
CG B:MET347 4.4 39.9 1.0
C10 B:6DE102 4.5 0.1 1.0
CG B:LEU393 4.5 37.3 1.0
C7 B:6DE102 4.5 0.0 1.0
O B:ASP392 4.5 36.9 1.0
CE B:MET347 4.7 42.6 1.0
CE2 B:PHE446 4.9 31.8 1.0
OD1 B:ASP392 4.9 33.5 1.0

Reference:

G.L.Card, L.Blasdel, B.P.England, C.Zhang, Y.Suzuki, S.Gillette, D.Fong, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. A Family of Phosphodiesterase Inhibitors Discovered By Cocrystallography and Scaffold-Based Drug Design Nat.Biotechnol. V. 23 201 2005.
ISSN: ISSN 1087-0156
PubMed: 15685167
DOI: 10.1038/NBT1059
Page generated: Sat Dec 12 08:55:06 2020

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