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Fluorine in PDB 5a86: Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist

Enzymatic activity of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist

All present enzymatic activity of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist:
2.3.1.48;

Protein crystallography data

The structure of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist, PDB code: 5a86 was solved by Y.Xue, L.Oster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.88 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.670, 89.200, 106.560, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 25.6

Other elements in 5a86:

The structure of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist (pdb code 5a86). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist, PDB code: 5a86:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 1 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:73.8
occ:1.00
 F27 A:D7E1433 0.0 73.8 1.0
C26 A:D7E1433 1.4 73.6 1.0
F28 A:D7E1433 2.2 75.1 1.0
F29 A:D7E1433 2.3 75.8 1.0
C6 A:D7E1433 2.4 69.8 1.0
C5 A:D7E1433 3.1 67.2 1.0
CB A:MET243 3.2 44.6 1.0
CG A:MET243 3.3 51.8 1.0
CA A:MET243 3.3 40.3 1.0
C7 A:D7E1433 3.5 69.2 1.0
N A:MET243 3.7 37.9 1.0
CD2 A:HIS242 3.9 38.1 1.0
O A:LEU239 4.2 42.1 1.0
C4 A:D7E1433 4.4 65.8 1.0
C A:HIS242 4.5 38.3 1.0
SD A:MET243 4.6 60.1 1.0
C A:MET243 4.7 40.6 1.0
CE1 A:TYR306 4.7 42.6 1.0
C8 A:D7E1433 4.7 67.8 1.0
CG A:HIS242 4.8 36.2 1.0
CG1 A:VAL211 4.8 72.5 1.0
NE2 A:HIS242 4.9 37.5 1.0
O A:HIS242 4.9 38.4 1.0
CB A:LEU239 4.9 41.9 1.0
CB A:HIS242 4.9 33.7 1.0

Fluorine binding site 2 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 2 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:75.1
occ:1.00
 F28 A:D7E1433 0.0 75.1 1.0
C26 A:D7E1433 1.4 73.6 1.0
F27 A:D7E1433 2.2 73.8 1.0
F29 A:D7E1433 2.3 75.8 1.0
C6 A:D7E1433 2.4 69.8 1.0
C5 A:D7E1433 2.9 67.2 1.0
CD1 A:TYR306 3.1 42.2 1.0
CE1 A:TYR306 3.1 42.6 1.0
CG1 A:VAL211 3.4 72.5 1.0
C7 A:D7E1433 3.5 69.2 1.0
CG A:TYR306 3.9 41.3 1.0
CZ A:TYR306 4.1 46.9 1.0
C4 A:D7E1433 4.2 65.8 1.0
CD2 A:HIS242 4.4 38.1 1.0
C8 A:D7E1433 4.6 67.8 1.0
CB A:TYR306 4.6 41.4 1.0
CL25 A:D7E1433 4.6 49.4 1.0
C21 A:D7E1433 4.6 50.2 1.0
CB A:VAL211 4.7 73.3 1.0
CD2 A:TYR306 4.7 41.5 1.0
OH A:TYR306 4.8 44.1 1.0
CE2 A:TYR306 4.8 41.4 1.0
NE2 A:HIS242 4.9 37.5 1.0
C9 A:D7E1433 4.9 66.0 1.0
CG2 A:VAL211 5.0 73.5 1.0

Fluorine binding site 3 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 3 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:75.8
occ:1.00
 F29 A:D7E1433 0.0 75.8 1.0
C26 A:D7E1433 1.4 73.6 1.0
F28 A:D7E1433 2.3 75.1 1.0
F27 A:D7E1433 2.3 73.8 1.0
C6 A:D7E1433 2.4 69.8 1.0
C7 A:D7E1433 2.7 69.2 1.0
CD2 A:HIS242 3.3 38.1 1.0
CE1 A:TYR306 3.3 42.6 1.0
CZ A:TYR306 3.6 46.9 1.0
OH A:TYR306 3.6 44.1 1.0
CB A:MET246 3.6 31.2 1.0
C5 A:D7E1433 3.7 67.2 1.0
NE2 A:HIS242 3.7 37.5 1.0
CG A:MET246 3.9 33.7 1.0
CA A:MET243 4.0 40.3 1.0
CD1 A:TYR306 4.0 42.2 1.0
C8 A:D7E1433 4.0 67.8 1.0
N A:MET243 4.4 37.9 1.0
CE2 A:TYR306 4.4 41.4 1.0
CG A:HIS242 4.5 36.2 1.0
O A:HIS242 4.5 38.4 1.0
CG A:MET243 4.6 51.8 1.0
CB A:MET243 4.6 44.6 1.0
C A:HIS242 4.7 38.3 1.0
C4 A:D7E1433 4.8 65.8 1.0
CG A:TYR306 4.8 41.3 1.0
CL25 A:D7E1433 4.9 49.4 1.0
CE1 A:HIS242 4.9 37.1 1.0
C9 A:D7E1433 4.9 66.0 1.0
O A:MET243 5.0 38.7 1.0
CD2 A:TYR306 5.0 41.5 1.0

Fluorine binding site 4 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 4 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1432

b:71.4
occ:1.00
 F27 B:D7E1432 0.0 71.4 1.0
C26 B:D7E1432 1.4 72.6 1.0
F28 B:D7E1432 2.3 71.9 1.0
F29 B:D7E1432 2.3 74.3 1.0
C6 B:D7E1432 2.4 72.6 1.0
C7 B:D7E1432 2.9 71.3 1.0
CA B:MET243 3.2 40.3 1.0
CB B:MET243 3.2 44.6 1.0
N B:MET243 3.4 37.8 1.0
CD2 B:HIS242 3.4 39.2 1.0
C5 B:D7E1432 3.5 73.7 1.0
CG B:MET243 3.6 50.9 1.0
O B:LEU239 3.8 45.5 1.0
C B:HIS242 4.1 39.8 1.0
C8 B:D7E1432 4.2 71.4 1.0
CG B:HIS242 4.2 38.0 1.0
CB B:HIS242 4.4 35.5 1.0
CE1 B:TYR306 4.4 36.6 1.0
NE2 B:HIS242 4.4 38.9 1.0
O B:HIS242 4.6 38.3 1.0
CB B:LEU239 4.6 43.2 1.0
C4 B:D7E1432 4.6 74.1 1.0
C B:MET243 4.6 43.7 1.0
CD2 B:LEU239 4.7 50.6 1.0
C B:LEU239 4.8 46.6 1.0
CD1 B:TYR306 4.8 36.0 1.0
CA B:HIS242 4.9 35.6 1.0
C9 B:D7E1432 4.9 73.5 1.0

Fluorine binding site 5 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 5 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1432

b:71.9
occ:1.00
 F28 B:D7E1432 0.0 71.9 1.0
C26 B:D7E1432 1.4 72.6 1.0
F29 B:D7E1432 2.3 74.3 1.0
F27 B:D7E1432 2.3 71.4 1.0
C6 B:D7E1432 2.4 72.6 1.0
CD1 B:TYR306 2.9 36.0 1.0
C7 B:D7E1432 3.0 71.3 1.0
CE1 B:TYR306 3.0 36.6 1.0
C5 B:D7E1432 3.4 73.7 1.0
CG2 B:VAL211 3.5 60.9 1.0
CG B:TYR306 3.9 36.3 1.0
CZ B:TYR306 4.1 44.0 1.0
CD2 B:HIS242 4.2 39.2 1.0
C8 B:D7E1432 4.3 71.4 1.0
CB B:TYR306 4.6 36.5 1.0
C4 B:D7E1432 4.6 74.1 1.0
NE2 B:HIS242 4.7 38.9 1.0
C21 B:D7E1432 4.8 59.8 1.0
CD2 B:TYR306 4.8 38.1 1.0
CL25 B:D7E1432 4.8 60.4 1.0
OH B:TYR306 4.9 39.7 1.0
CB B:VAL211 4.9 61.6 1.0
CE2 B:TYR306 4.9 39.1 1.0
C9 B:D7E1432 4.9 73.5 1.0

Fluorine binding site 6 out of 6 in 5a86

Go back to Fluorine Binding Sites List in 5a86
Fluorine binding site 6 out of 6 in the Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Pregnane X Receptor in Complex with A Sphingosine 1- Phosphate Receptor 1 Antagonist within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1432

b:74.3
occ:1.00
 F29 B:D7E1432 0.0 74.3 1.0
C26 B:D7E1432 1.4 72.6 1.0
F28 B:D7E1432 2.3 71.9 1.0
F27 B:D7E1432 2.3 71.4 1.0
C6 B:D7E1432 2.4 72.6 1.0
C5 B:D7E1432 2.7 73.7 1.0
CG2 B:VAL211 3.5 60.9 1.0
C7 B:D7E1432 3.7 71.3 1.0
CD1 B:LEU209 4.0 95.2 1.0
C4 B:D7E1432 4.1 74.1 1.0
CB B:LEU239 4.1 43.2 1.0
CD1 B:LEU239 4.2 49.3 1.0
CG B:MET243 4.3 50.9 1.0
CB B:MET243 4.4 44.6 1.0
CG B:LEU239 4.6 48.9 1.0
O B:LEU239 4.6 45.5 1.0
CD2 B:LEU239 4.7 50.6 1.0
C8 B:D7E1432 4.8 71.4 1.0
C9 B:D7E1432 5.0 73.5 1.0

Reference:

E.J.Hennessy, V.B.Oza, A.Adam, K.Byth, L.Castriotta, G.Grewal, G.Hamilton, V.M.Kamhi, P.Lewis, D.Li, P.D.Lyne, L.Oster, M.T.Rooney, J.C.Saeh, L.Sha, Q.Su, S.Wen, Y.Xue, B.Yang. Identification and Optimization of Benzimidazole Sulfonamides As Orally Bioavailable Sphingosine 1-Phosphate Receptor 1 Antagonists with in Vivo Activity. J.Med.Chem. V. 58 7057 2015.
ISSN: ISSN 0022-2623
PubMed: 26291341
DOI: 10.1021/ACS.JMEDCHEM.5B01078
Page generated: Tue Jul 15 02:10:11 2025

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