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Chlorine in PDB 3ly2: Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor, PDB code: 3ly2 was solved by A.K.Shiau, A.R.Coyle, J.H.Hsien, L.M.Staszewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.84 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 214.796, 233.964, 165.258, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3ly2:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Zinc (Zn) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Chlorine atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor (pdb code 3ly2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor, PDB code: 3ly2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 1 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1000

b:71.4
occ:1.00
 CL20 A:Z721000 0.0 71.4 1.0
C19 A:Z721000 1.7 68.6 1.0
C18 A:Z721000 2.7 67.5 1.0
C21 A:Z721000 2.7 69.8 1.0
N16 A:Z721000 2.9 65.3 1.0
O A:HOH1009 3.2 22.1 1.0
CD2 A:LEU393 3.2 26.6 1.0
OD1 A:ASP392 3.3 20.1 1.0
CG A:ASP392 3.3 20.7 1.0
O A:HOH2057 3.6 28.6 1.0
O A:HOH1008 3.6 21.7 1.0
OD2 A:ASP392 3.7 20.1 1.0
CG A:LEU393 3.8 26.2 1.0
O A:ASP392 3.8 24.7 1.0
CB A:ASP392 3.8 24.5 1.0
C15 A:Z721000 3.9 60.8 1.0
C24 A:Z721000 3.9 68.5 1.0
N22 A:Z721000 4.0 70.3 1.0
C A:ASP392 4.1 24.1 1.0
C17 A:Z721000 4.4 60.5 1.0
SD A:MET347 4.5 49.4 1.0
C23 A:Z721000 4.5 69.6 1.0
N A:LEU393 4.5 23.8 1.0
CA A:ASP392 4.6 24.2 1.0
CG A:MET347 4.6 42.1 1.0
O A:HOH1007 4.6 23.8 1.0
CA A:LEU393 4.7 24.1 1.0
CB A:LEU393 4.8 24.2 1.0
ZN A:ZN1001 4.8 27.9 1.0
C14 A:Z721000 4.8 59.9 1.0
CD1 A:LEU393 4.9 27.8 1.0
O A:THR345 4.9 27.0 1.0
C13 A:Z721000 5.0 59.5 1.0

Chlorine binding site 2 out of 16 in 3ly2

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Chlorine binding site 2 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1000

b:68.6
occ:1.00
 CL25 A:Z721000 0.0 68.6 1.0
C24 A:Z721000 1.7 68.5 1.0
C18 A:Z721000 2.7 67.5 1.0
C23 A:Z721000 2.7 69.6 1.0
N16 A:Z721000 2.9 65.3 1.0
C15 A:Z721000 3.2 60.8 1.0
C17 A:Z721000 3.3 60.5 1.0
O A:HOH2310 3.4 41.0 1.0
CE1 A:HIS234 3.8 26.5 1.0
C19 A:Z721000 3.9 68.6 1.0
NE2 A:HIS234 3.9 27.9 1.0
N22 A:Z721000 4.0 70.3 1.0
C14 A:Z721000 4.1 59.9 1.0
CD1 A:ILE410 4.1 32.0 1.0
CA A:Z721000 4.2 59.8 1.0
CZ A:PHE414 4.3 42.1 1.0
CE1 A:PHE414 4.3 41.5 1.0
O A:HOH1008 4.4 21.7 1.0
C21 A:Z721000 4.5 69.8 1.0
O A:HOH1006 4.5 15.8 1.0
O A:HOH2071 4.6 42.5 1.0
C13 A:Z721000 4.8 59.5 1.0
C1 A:Z721000 4.8 59.7 1.0
O A:HOH1009 4.8 22.1 1.0
OA A:Z721000 4.8 58.8 1.0
OB A:Z721000 4.9 59.3 1.0

Chlorine binding site 3 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 3 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1000

b:60.4
occ:1.00
 CL20 B:Z721000 0.0 60.4 1.0
C19 B:Z721000 1.7 58.8 1.0
C18 B:Z721000 2.7 58.3 1.0
C21 B:Z721000 2.7 59.1 1.0
N16 B:Z721000 3.0 56.5 1.0
O B:HOH1009 3.0 15.5 1.0
OD1 B:ASP392 3.1 20.9 1.0
CG B:ASP392 3.3 21.6 1.0
CD2 B:LEU393 3.4 24.7 1.0
O B:HOH2033 3.4 36.3 1.0
O B:ASP392 3.7 26.2 1.0
CG B:LEU393 3.8 26.1 1.0
OD2 B:ASP392 3.8 20.6 1.0
CB B:ASP392 3.8 21.7 1.0
O B:HOH1008 3.9 21.6 1.0
C24 B:Z721000 4.0 58.4 1.0
C15 B:Z721000 4.0 54.4 1.0
C B:ASP392 4.0 24.1 1.0
N22 B:Z721000 4.0 58.5 1.0
SD B:MET347 4.2 42.2 1.0
C17 B:Z721000 4.5 54.9 1.0
N B:LEU393 4.5 24.2 1.0
C23 B:Z721000 4.5 57.7 1.0
CA B:ASP392 4.5 23.7 1.0
O B:HOH1007 4.6 21.1 1.0
CG B:MET347 4.6 36.6 1.0
CD1 B:LEU393 4.7 24.4 1.0
CA B:LEU393 4.8 24.9 1.0
CB B:LEU393 4.8 24.4 1.0
ZN B:ZN1001 4.9 27.4 1.0
C14 B:Z721000 4.9 53.6 1.0
O B:THR345 5.0 26.5 1.0

Chlorine binding site 4 out of 16 in 3ly2

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Chlorine binding site 4 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1000

b:57.2
occ:1.00
 CL25 B:Z721000 0.0 57.2 1.0
C24 B:Z721000 1.7 58.4 1.0
C18 B:Z721000 2.7 58.3 1.0
C23 B:Z721000 2.7 57.7 1.0
N16 B:Z721000 3.0 56.5 1.0
C15 B:Z721000 3.2 54.4 1.0
C17 B:Z721000 3.2 54.9 1.0
C19 B:Z721000 4.0 58.8 1.0
CE1 B:HIS234 4.0 25.9 1.0
N22 B:Z721000 4.0 58.5 1.0
C14 B:Z721000 4.1 53.6 1.0
CA B:Z721000 4.1 54.0 1.0
NE2 B:HIS234 4.1 26.5 1.0
CD1 B:ILE410 4.3 24.3 1.0
O B:HOH2051 4.4 29.9 1.0
CE1 B:PHE414 4.4 35.7 1.0
CZ B:PHE414 4.5 36.0 1.0
C21 B:Z721000 4.5 59.1 1.0
O B:HOH1006 4.7 13.7 1.0
O B:HOH1008 4.7 21.6 1.0
O B:HOH1009 4.8 15.5 1.0
C13 B:Z721000 4.8 52.9 1.0
C1 B:Z721000 4.8 53.0 1.0
OB B:Z721000 4.8 54.7 1.0
OA B:Z721000 4.8 53.6 1.0

Chlorine binding site 5 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 5 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1000

b:61.4
occ:1.00
 CL20 C:Z721000 0.0 61.4 1.0
C19 C:Z721000 1.7 59.3 1.0
C18 C:Z721000 2.7 59.2 1.0
C21 C:Z721000 2.7 59.7 1.0
N16 C:Z721000 3.0 57.2 1.0
O C:HOH1009 3.1 26.0 1.0
OD1 C:ASP392 3.3 27.5 1.0
CD2 C:LEU393 3.3 29.6 1.0
CG C:ASP392 3.3 29.4 1.0
O C:ASP392 3.6 31.0 1.0
CG C:LEU393 3.6 28.3 1.0
O C:HOH2016 3.7 26.9 1.0
OD2 C:ASP392 3.8 29.7 1.0
CB C:ASP392 3.8 29.6 1.0
C C:ASP392 3.9 30.0 1.0
O C:HOH1008 3.9 27.7 1.0
C15 C:Z721000 4.0 54.1 1.0
C24 C:Z721000 4.0 60.1 1.0
N22 C:Z721000 4.0 59.8 1.0
SD C:MET347 4.1 42.9 1.0
N C:LEU393 4.3 29.3 1.0
C17 C:Z721000 4.4 53.4 1.0
CA C:ASP392 4.5 29.9 1.0
C23 C:Z721000 4.5 59.5 1.0
CA C:LEU393 4.6 29.4 1.0
CB C:LEU393 4.6 28.5 1.0
CG C:MET347 4.6 37.9 1.0
CD1 C:LEU393 4.7 27.0 1.0
O C:HOH1007 4.8 28.8 1.0
C14 C:Z721000 4.9 53.2 1.0
ZN C:ZN1001 5.0 33.1 1.0

Chlorine binding site 6 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 6 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1000

b:61.7
occ:1.00
 CL25 C:Z721000 0.0 61.7 1.0
C24 C:Z721000 1.7 60.1 1.0
C18 C:Z721000 2.7 59.2 1.0
C23 C:Z721000 2.7 59.5 1.0
N16 C:Z721000 3.0 57.2 1.0
C15 C:Z721000 3.2 54.1 1.0
C17 C:Z721000 3.3 53.4 1.0
CE1 C:HIS234 3.8 26.8 1.0
NE2 C:HIS234 3.9 26.6 1.0
C19 C:Z721000 3.9 59.3 1.0
N22 C:Z721000 4.0 59.8 1.0
O C:HOH2367 4.1 40.8 1.0
C14 C:Z721000 4.1 53.2 1.0
CA C:Z721000 4.2 53.8 1.0
CD1 C:ILE410 4.3 33.3 1.0
O C:HOH1006 4.4 22.7 1.0
CZ C:PHE414 4.4 39.4 1.0
C21 C:Z721000 4.5 59.7 1.0
CE1 C:PHE414 4.5 39.1 1.0
O C:HOH1008 4.5 27.7 1.0
C13 C:Z721000 4.8 52.0 1.0
C1 C:Z721000 4.9 53.0 1.0
OA C:Z721000 4.9 53.4 1.0
OB C:Z721000 4.9 54.3 1.0

Chlorine binding site 7 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 7 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1000

b:64.1
occ:1.00
 CL20 D:Z721000 0.0 64.1 1.0
C19 D:Z721000 1.7 64.0 1.0
C18 D:Z721000 2.7 63.3 1.0
C21 D:Z721000 2.7 65.3 1.0
N16 D:Z721000 2.9 60.5 1.0
CD2 D:LEU393 3.2 26.7 1.0
OD1 D:ASP392 3.2 26.3 1.0
O D:HOH1009 3.3 29.6 1.0
CG D:ASP392 3.5 25.6 1.0
CG D:LEU393 3.6 26.4 1.0
O D:HOH2036 3.7 23.2 1.0
O D:HOH1008 3.7 26.9 1.0
O D:ASP392 3.7 25.5 1.0
C15 D:Z721000 3.9 56.6 1.0
CB D:ASP392 3.9 24.2 1.0
C24 D:Z721000 3.9 65.2 1.0
N22 D:Z721000 4.0 65.8 1.0
C D:ASP392 4.0 25.9 1.0
OD2 D:ASP392 4.0 24.7 1.0
SD D:MET347 4.2 46.5 1.0
C17 D:Z721000 4.3 55.2 1.0
N D:LEU393 4.4 26.4 1.0
C23 D:Z721000 4.5 65.8 1.0
CA D:ASP392 4.6 25.0 1.0
CD1 D:LEU393 4.6 25.7 1.0
CA D:LEU393 4.7 27.1 1.0
O D:HOH1007 4.7 26.5 1.0
CB D:LEU393 4.7 25.9 1.0
CG D:MET347 4.7 41.5 1.0
C14 D:Z721000 4.8 56.0 1.0

Chlorine binding site 8 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 8 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1000

b:68.9
occ:1.00
 CL25 D:Z721000 0.0 68.9 1.0
C24 D:Z721000 1.7 65.2 1.0
C18 D:Z721000 2.7 63.3 1.0
C23 D:Z721000 2.7 65.8 1.0
N16 D:Z721000 3.0 60.5 1.0
C15 D:Z721000 3.2 56.6 1.0
C17 D:Z721000 3.3 55.2 1.0
CE1 D:HIS234 3.6 30.0 1.0
NE2 D:HIS234 3.7 31.2 1.0
C19 D:Z721000 3.9 64.0 1.0
N22 D:Z721000 4.0 65.8 1.0
CD1 D:ILE410 4.1 30.2 1.0
C14 D:Z721000 4.1 56.0 1.0
CA D:Z721000 4.2 54.0 1.0
O D:HOH2385 4.3 43.7 1.0
CE1 D:PHE414 4.3 36.7 1.0
O D:HOH1006 4.4 19.9 1.0
O D:HOH2386 4.4 41.9 1.0
C21 D:Z721000 4.5 65.3 1.0
O D:HOH1008 4.5 26.9 1.0
CZ D:PHE414 4.5 39.2 1.0
C13 D:Z721000 4.8 55.4 1.0
C1 D:Z721000 4.9 55.3 1.0
ND1 D:HIS234 4.9 31.4 1.0
OB D:Z721000 4.9 53.1 1.0
OA D:Z721000 4.9 53.0 1.0

Chlorine binding site 9 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 9 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1000

b:59.9
occ:1.00
 CL20 E:Z721000 0.0 59.9 1.0
C19 E:Z721000 1.7 59.5 1.0
C18 E:Z721000 2.7 59.7 1.0
C21 E:Z721000 2.7 59.4 1.0
N16 E:Z721000 3.0 57.3 1.0
O E:HOH1009 3.1 30.4 1.0
CD2 E:LEU393 3.2 29.8 1.0
OD1 E:ASP392 3.3 29.3 1.0
CG E:ASP392 3.4 29.8 1.0
CG E:LEU393 3.6 28.9 1.0
O E:ASP392 3.6 31.2 1.0
O E:HOH2049 3.7 27.9 1.0
OD2 E:ASP392 3.8 29.4 1.0
CB E:ASP392 3.8 30.2 1.0
C E:ASP392 3.9 29.8 1.0
C15 E:Z721000 3.9 55.5 1.0
C24 E:Z721000 4.0 60.9 1.0
O E:HOH1008 4.0 30.0 1.0
N22 E:Z721000 4.0 60.5 1.0
SD E:MET347 4.1 42.8 1.0
N E:LEU393 4.3 28.7 1.0
C17 E:Z721000 4.4 55.7 1.0
CA E:ASP392 4.5 30.6 1.0
C23 E:Z721000 4.5 60.5 1.0
CA E:LEU393 4.5 29.2 1.0
CB E:LEU393 4.6 29.8 1.0
CG E:MET347 4.6 39.2 1.0
CD1 E:LEU393 4.6 28.3 1.0
O E:HOH1007 4.8 31.2 1.0
C14 E:Z721000 4.9 55.0 1.0

Chlorine binding site 10 out of 16 in 3ly2

Go back to Chlorine Binding Sites List in 3ly2
Chlorine binding site 10 out of 16 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1000

b:62.9
occ:1.00
 CL25 E:Z721000 0.0 62.9 1.0
C24 E:Z721000 1.7 60.9 1.0
C18 E:Z721000 2.7 59.7 1.0
C23 E:Z721000 2.7 60.5 1.0
N16 E:Z721000 3.0 57.3 1.0
C15 E:Z721000 3.2 55.5 1.0
C17 E:Z721000 3.2 55.7 1.0
CE1 E:HIS234 3.8 26.6 1.0
NE2 E:HIS234 3.9 27.4 1.0
C19 E:Z721000 3.9 59.5 1.0
N22 E:Z721000 4.0 60.5 1.0
C14 E:Z721000 4.1 55.0 1.0
CA E:Z721000 4.2 56.0 1.0
CD1 E:ILE410 4.3 34.7 1.0
O E:HOH1006 4.4 25.4 1.0
CZ E:PHE414 4.4 39.0 1.0
O E:HOH2096 4.5 35.0 1.0
C21 E:Z721000 4.5 59.4 1.0
CE1 E:PHE414 4.5 37.8 1.0
O E:HOH1008 4.5 30.0 1.0
C13 E:Z721000 4.8 53.8 1.0
C1 E:Z721000 4.9 54.8 1.0
OA E:Z721000 4.9 55.9 1.0
OB E:Z721000 4.9 55.8 1.0
O E:HOH1009 5.0 30.4 1.0

Reference:

S.P.Govek, G.Oshiro, J.V.Anzola, C.Beauregard, J.Chen, A.R.Coyle, D.A.Gamache, M.R.Hellberg, J.N.Hsien, J.M.Lerch, J.C.Liao, J.W.Malecha, L.M.Staszewski, D.J.Thomas, J.M.Yanni, S.A.Noble, A.K.Shiau. Water-Soluble PDE4 Inhibitors For the Treatment of Dry Eye. Bioorg.Med.Chem.Lett. V. 20 2928 2010.
ISSN: ISSN 0960-894X
PubMed: 20378348
DOI: 10.1016/J.BMCL.2010.03.023
Page generated: Fri Jul 11 07:37:18 2025

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