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Fluorine in PDB 1xoq: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast

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

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast, PDB code: 1xoq 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) 81.65 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.899, 60.116, 163.996, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.5

Other elements in 1xoq:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 4 in 1xoq

Go back to Fluorine Binding Sites List in 1xoq
Fluorine binding site 1 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:14.8
occ:1.00
 F18 A:ROF502 0.0 14.8 1.0
C16 A:ROF502 1.3 14.7 1.0
F17 A:ROF502 2.2 15.0 1.0
O15 A:ROF502 2.2 13.9 1.0
C12 A:ROF502 2.9 13.9 1.0
C11 A:ROF502 2.9 12.6 1.0
C A:TRP332 3.2 5.8 1.0
N A:THR333 3.2 6.5 1.0
O A:TRP332 3.3 4.6 1.0
CB A:TRP332 3.4 6.2 1.0
CA A:THR333 3.4 6.2 1.0
OD1 A:ASN321 3.4 6.1 1.0
OG1 A:THR333 3.7 5.5 1.0
CG2 A:ILE336 3.9 8.0 1.0
CA A:TRP332 3.9 5.9 1.0
CB A:ASN321 3.9 6.0 1.0
CG A:ASN321 4.1 5.9 1.0
CB A:THR333 4.2 6.2 1.0
C13 A:ROF502 4.2 13.2 1.0
CE1 A:TYR159 4.3 5.2 1.0
C10 A:ROF502 4.3 14.1 1.0
CB A:ILE336 4.3 7.2 1.0
O A:TYR329 4.5 5.2 1.0
CE1 A:TYR329 4.5 4.4 1.0
CD1 A:TYR329 4.6 3.4 1.0
C A:THR333 4.7 7.0 1.0
CG A:TRP332 4.7 5.9 1.0
NE2 A:GLN369 4.7 6.2 1.0
OE1 A:GLN369 4.7 4.6 1.0
O19 A:ROF502 4.8 15.0 1.0
CD1 A:TYR159 4.9 5.4 1.0

Fluorine binding site 2 out of 4 in 1xoq

Go back to Fluorine Binding Sites List in 1xoq
Fluorine binding site 2 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:15.0
occ:1.00
 F17 A:ROF502 0.0 15.0 1.0
C16 A:ROF502 1.3 14.7 1.0
F18 A:ROF502 2.2 14.8 1.0
O15 A:ROF502 2.3 13.9 1.0
C12 A:ROF502 2.8 13.9 1.0
C11 A:ROF502 3.0 12.6 1.0
CB A:ASN321 3.3 6.0 1.0
CE1 A:TYR329 3.5 4.4 1.0
CG A:PRO322 3.6 4.7 1.0
OD1 A:ASN321 3.7 6.1 1.0
CD A:PRO322 3.7 5.2 1.0
OE1 A:GLN369 3.7 4.6 1.0
CE2 A:PHE372 3.8 9.1 1.0
CD1 A:TYR329 3.9 3.4 1.0
CG A:ASN321 4.0 5.9 1.0
C13 A:ROF502 4.0 13.2 1.0
N A:PRO322 4.2 4.8 1.0
C10 A:ROF502 4.2 14.1 1.0
O A:HOH1017 4.3 11.6 1.0
OG1 A:THR333 4.3 5.5 1.0
CD2 A:PHE372 4.4 8.2 1.0
CA A:ASN321 4.4 5.8 1.0
CD A:GLN369 4.5 4.4 1.0
C A:ASN321 4.5 5.1 1.0
O19 A:ROF502 4.5 15.0 1.0
NE2 A:GLN369 4.6 6.2 1.0
CZ A:TYR329 4.6 3.9 1.0
CB A:TRP332 4.7 6.2 1.0
CZ A:PHE372 4.8 8.3 1.0
CB A:PRO322 4.8 4.8 1.0
OH A:TYR329 4.8 4.7 1.0
CA A:PRO322 4.9 4.6 1.0
C14 A:ROF502 5.0 13.3 1.0
N A:THR333 5.0 6.5 1.0

Fluorine binding site 3 out of 4 in 1xoq

Go back to Fluorine Binding Sites List in 1xoq
Fluorine binding site 3 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:13.5
occ:1.00
 F18 B:ROF501 0.0 13.5 1.0
C16 B:ROF501 1.3 13.3 1.0
O15 B:ROF501 2.2 12.6 1.0
F17 B:ROF501 2.2 14.1 1.0
C12 B:ROF501 2.9 12.5 1.0
C11 B:ROF501 3.0 11.6 1.0
C B:TRP332 3.2 5.5 1.0
O B:TRP332 3.2 5.9 1.0
N B:THR333 3.2 5.1 1.0
CA B:THR333 3.4 4.5 1.0
OD1 B:ASN321 3.4 9.1 1.0
CB B:TRP332 3.5 5.9 1.0
OG1 B:THR333 3.6 3.4 1.0
CG2 B:ILE336 3.8 6.1 1.0
CA B:TRP332 4.0 5.5 1.0
CB B:ASN321 4.0 6.1 1.0
CG B:ASN321 4.1 6.1 1.0
CB B:THR333 4.1 4.3 1.0
C13 B:ROF501 4.2 12.9 1.0
CB B:ILE336 4.3 6.6 1.0
C10 B:ROF501 4.3 12.3 1.0
CE1 B:TYR159 4.3 6.1 1.0
CE1 B:TYR329 4.5 3.3 1.0
O B:TYR329 4.6 4.9 1.0
C B:THR333 4.6 5.0 1.0
CD1 B:TYR329 4.7 3.0 1.0
OE1 B:GLN369 4.7 3.5 1.0
CG B:TRP332 4.7 5.8 1.0
O19 B:ROF501 4.8 13.8 1.0
NE2 B:GLN369 4.8 3.1 1.0
CG2 B:THR333 5.0 4.5 1.0
CD1 B:TYR159 5.0 5.1 1.0

Fluorine binding site 4 out of 4 in 1xoq

Go back to Fluorine Binding Sites List in 1xoq
Fluorine binding site 4 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Roflumilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:14.1
occ:1.00
 F17 B:ROF501 0.0 14.1 1.0
C16 B:ROF501 1.3 13.3 1.0
F18 B:ROF501 2.2 13.5 1.0
O15 B:ROF501 2.3 12.6 1.0
C12 B:ROF501 2.8 12.5 1.0
C11 B:ROF501 3.0 11.6 1.0
CB B:ASN321 3.2 6.1 1.0
CE1 B:TYR329 3.4 3.3 1.0
CG B:PRO322 3.6 5.4 1.0
OD1 B:ASN321 3.6 9.1 1.0
OE1 B:GLN369 3.7 3.5 1.0
CD B:PRO322 3.7 5.0 1.0
CE2 B:PHE372 3.7 10.5 1.0
CD1 B:TYR329 3.9 3.0 1.0
CG B:ASN321 3.9 6.1 1.0
C13 B:ROF501 4.1 12.9 1.0
N B:PRO322 4.1 5.2 1.0
OG1 B:THR333 4.2 3.4 1.0
O B:HOH2020 4.2 10.6 1.0
C10 B:ROF501 4.3 12.3 1.0
CD2 B:PHE372 4.3 9.3 1.0
CA B:ASN321 4.4 5.8 1.0
C B:ASN321 4.4 5.4 1.0
CD B:GLN369 4.5 4.9 1.0
CZ B:TYR329 4.5 5.2 1.0
O19 B:ROF501 4.6 13.8 1.0
NE2 B:GLN369 4.6 3.1 1.0
CB B:PRO322 4.7 4.9 1.0
CB B:TRP332 4.7 5.9 1.0
OH B:TYR329 4.7 3.8 1.0
CZ B:PHE372 4.8 10.3 1.0
CA B:PRO322 4.9 4.7 1.0
N B:THR333 5.0 5.1 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: Wed Jul 31 13:24:15 2024

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