Atomistry » Fluorine » PDB 5o6j-5olv » 5ohj
Atomistry »
  Fluorine »
    PDB 5o6j-5olv »
      5ohj »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy