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Fluorine in PDB 5ohj: Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.

Enzymatic activity of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.

All present enzymatic activity of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.:
3.1.4.53;

Protein crystallography data

The structure of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj was solved by A.Rizzi, L.Carzaniga, E.Armani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.61 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.270, 55.730, 225.560, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.2

Other elements in 5ohj:

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

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. (pdb code 5ohj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5ohj

Go back to Fluorine Binding Sites List in 5ohj
Fluorine binding site 1 out of 4 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:18.4
occ:1.00
 F A:9VE801 0.0 18.4 1.0
C A:9VE801 1.3 14.1 1.0
O A:9VE801 2.2 13.6 1.0
F1 A:9VE801 2.2 16.5 1.0
C1 A:9VE801 2.9 16.0 1.0
C31 A:9VE801 3.0 15.4 1.0
ND2 A:ASN567 3.2 10.6 1.0
C A:TRP578 3.2 12.1 1.0
CB A:TRP578 3.4 11.5 1.0
O A:TRP578 3.4 12.1 1.0
N A:THR579 3.4 11.4 1.0
CA A:THR579 3.6 12.9 1.0
OG1 A:THR579 3.8 12.4 1.0
CB A:ASN567 3.9 11.5 1.0
CG2 A:ILE582 3.9 13.0 1.0
CA A:TRP578 3.9 11.6 1.0
CG A:ASN567 4.0 11.3 1.0
CE2 A:TYR405 4.2 10.3 1.0
C2 A:9VE801 4.2 15.3 1.0
C30 A:9VE801 4.4 14.7 1.0
CB A:THR579 4.4 12.6 1.0
CB A:ILE582 4.4 12.5 1.0
O A:TYR575 4.6 12.1 1.0
CG A:TRP578 4.7 11.7 1.0
CE1 A:TYR575 4.7 11.2 1.0
O1 A:9VE801 4.7 16.2 1.0
CD1 A:TYR575 4.7 11.5 1.0
C A:THR579 4.9 13.7 1.0
OH A:TYR405 4.9 10.5 1.0
OE1 A:GLN615 4.9 12.1 1.0
CD2 A:TYR405 4.9 10.4 1.0
CZ A:TYR405 4.9 9.8 1.0
NE2 A:GLN615 5.0 12.4 1.0

Fluorine binding site 2 out of 4 in 5ohj

Go back to Fluorine Binding Sites List in 5ohj
Fluorine binding site 2 out of 4 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:16.5
occ:1.00
 F1 A:9VE801 0.0 16.5 1.0
C A:9VE801 1.3 14.1 1.0
F A:9VE801 2.2 18.4 1.0
O A:9VE801 2.3 13.6 1.0
C1 A:9VE801 2.8 16.0 1.0
C31 A:9VE801 3.0 15.4 1.0
CB A:ASN567 3.3 11.5 1.0
CE1 A:TYR575 3.4 11.2 1.0
CG A:PRO568 3.6 10.6 1.0
ND2 A:ASN567 3.7 10.6 1.0
CD A:PRO568 3.7 10.3 1.0
CE2 A:PHE618 3.7 13.4 1.0
OE1 A:GLN615 3.7 12.1 1.0
CD1 A:TYR575 3.9 11.5 1.0
CG A:ASN567 4.1 11.3 1.0
C2 A:9VE801 4.1 15.3 1.0
N A:PRO568 4.2 10.6 1.0
C30 A:9VE801 4.2 14.7 1.0
OG1 A:THR579 4.3 12.4 1.0
O A:HOH759 4.3 14.0 1.0
CD2 A:PHE618 4.4 14.4 1.0
CA A:ASN567 4.4 10.3 1.0
CZ A:TYR575 4.5 12.0 1.0
C A:ASN567 4.5 10.8 1.0
CD A:GLN615 4.5 12.1 1.0
O1 A:9VE801 4.5 16.2 1.0
NE2 A:GLN615 4.7 12.4 1.0
CZ A:PHE618 4.7 13.1 1.0
CB A:TRP578 4.8 11.5 1.0
OH A:TYR575 4.8 12.9 1.0
CB A:PRO568 4.8 12.5 1.0
CA A:PRO568 4.9 11.4 1.0

Fluorine binding site 3 out of 4 in 5ohj

Go back to Fluorine Binding Sites List in 5ohj
Fluorine binding site 3 out of 4 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:20.1
occ:1.00
 F B:9VE801 0.0 20.1 1.0
C B:9VE801 1.3 19.0 1.0
O B:9VE801 2.1 17.6 1.0
F1 B:9VE801 2.3 19.3 1.0
C1 B:9VE801 2.8 18.1 1.0
C31 B:9VE801 3.0 17.6 1.0
C B:TRP578 3.2 14.2 1.0
O B:TRP578 3.2 12.9 1.0
ND2 B:ASN567 3.3 13.1 1.0
CB B:TRP578 3.4 13.5 1.0
N B:THR579 3.4 14.3 1.0
CA B:THR579 3.6 14.7 1.0
CG2 B:ILE582 3.8 14.3 1.0
OG1 B:THR579 3.9 13.0 1.0
CA B:TRP578 3.9 13.7 1.0
CB B:ASN567 4.0 12.6 1.0
C2 B:9VE801 4.1 18.8 1.0
CG B:ASN567 4.1 13.4 1.0
CE2 B:TYR405 4.2 13.8 1.0
CB B:ILE582 4.3 14.0 1.0
C30 B:9VE801 4.3 17.5 1.0
CB B:THR579 4.4 14.7 1.0
O1 B:9VE801 4.6 19.0 1.0
CE1 B:TYR575 4.7 13.6 1.0
CG B:TRP578 4.7 13.8 1.0
O B:TYR575 4.7 14.5 1.0
CD1 B:TYR575 4.8 13.6 1.0
C B:THR579 4.8 16.0 1.0
OE1 B:GLN615 4.9 13.3 1.0
OH B:TYR405 4.9 13.5 1.0
NE2 B:GLN615 4.9 13.6 1.0
CD2 B:TYR405 4.9 14.3 1.0
CZ B:TYR405 4.9 13.4 1.0

Fluorine binding site 4 out of 4 in 5ohj

Go back to Fluorine Binding Sites List in 5ohj
Fluorine binding site 4 out of 4 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:19.3
occ:1.00
 F1 B:9VE801 0.0 19.3 1.0
C B:9VE801 1.4 19.0 1.0
O B:9VE801 2.2 17.6 1.0
F B:9VE801 2.3 20.1 1.0
C1 B:9VE801 2.8 18.1 1.0
C31 B:9VE801 2.9 17.6 1.0
CB B:ASN567 3.3 12.6 1.0
CE1 B:TYR575 3.4 13.6 1.0
CG B:PRO568 3.5 11.6 1.0
OE1 B:GLN615 3.6 13.3 1.0
CE2 B:PHE618 3.7 13.8 1.0
CD B:PRO568 3.7 11.3 1.0
ND2 B:ASN567 3.7 13.1 1.0
CD1 B:TYR575 3.9 13.6 1.0
C2 B:9VE801 4.0 18.8 1.0
CG B:ASN567 4.1 13.4 1.0
C30 B:9VE801 4.2 17.5 1.0
N B:PRO568 4.2 11.4 1.0
OG1 B:THR579 4.3 13.0 1.0
CD2 B:PHE618 4.3 13.8 1.0
CD B:GLN615 4.4 13.5 1.0
CA B:ASN567 4.5 11.9 1.0
O1 B:9VE801 4.5 19.0 1.0
CZ B:TYR575 4.5 13.3 1.0
O B:HOH708 4.5 15.4 1.0
C B:ASN567 4.5 11.6 1.0
NE2 B:GLN615 4.6 13.6 1.0
CZ B:PHE618 4.7 14.1 1.0
CB B:TRP578 4.7 13.5 1.0
OH B:TYR575 4.8 14.2 1.0
CB B:PRO568 4.8 11.9 1.0
CA B:PRO568 4.9 11.6 1.0

Reference:

L.Carzaniga, G.Amari, A.Rizzi, C.Capaldi, R.De Fanti, E.Ghidini, G.Villetti, C.Carnini, N.Moretto, F.Facchinetti, P.Caruso, G.Marchini, L.Battipaglia, R.Patacchini, V.Cenacchi, R.Volta, F.Amadei, A.Pappani, S.Capacchi, V.Bagnacani, M.Delcanale, P.Puccini, S.Catinella, M.Civelli, E.Armani. Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives As Inhaled PDE4 Inhibitors For Respiratory Diseases. J. Med. Chem. V. 60 10026 2017.
ISSN: ISSN 1520-4804
PubMed: 29200281
DOI: 10.1021/ACS.JMEDCHEM.7B01044
Page generated: Thu Aug 1 12:24:57 2024

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