Fluorine in PDB 5tto: X-Ray Crystal Structure of Ppargamma in Complex with SR1643

Protein crystallography data

The structure of X-Ray Crystal Structure of Ppargamma in Complex with SR1643, PDB code: 5tto was solved by J.B.Bruning, R.L.Frkic, P.Griffin, T.Kamenecka, A.Abell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.50 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.110, 62.240, 118.880, 90.00, 102.20, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 5tto:

The structure of X-Ray Crystal Structure of Ppargamma in Complex with SR1643 also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643 (pdb code 5tto). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643, PDB code: 5tto:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5tto

Go back to Fluorine Binding Sites List in 5tto
Fluorine binding site 1 out of 4 in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Ppargamma in Complex with SR1643 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:74.7
occ:1.00
F30 A:7KK501 0.0 74.7 1.0
C25 A:7KK501 1.4 65.8 1.0
C26 A:7KK501 2.4 67.7 1.0
C22 A:7KK501 2.4 67.8 1.0
S21 A:7KK501 3.0 68.4 1.0
O23 A:7KK501 3.1 77.3 1.0
N20 A:7KK501 3.3 63.6 1.0
CE1 A:HIS449 3.5 66.5 1.0
CD1 A:PHE363 3.6 72.8 1.0
C29 A:7KK501 3.6 65.8 1.0
C27 A:7KK501 3.7 69.2 1.0
O A:HOH675 3.8 65.9 1.0
CG A:PHE363 3.9 70.0 1.0
CE1 A:PHE363 4.1 70.3 1.0
C28 A:7KK501 4.1 66.1 1.0
CB A:PHE363 4.1 66.5 1.0
CB A:CYS285 4.2 58.7 0.9
CB A:CYS285 4.2 58.9 0.1
CE2 A:PHE282 4.2 72.0 1.0
C15 A:7KK501 4.3 66.6 1.0
NE2 A:HIS449 4.4 69.7 1.0
ND1 A:HIS449 4.4 65.0 1.0
SG A:CYS285 4.4 67.8 1.0
CD2 A:PHE282 4.4 67.3 1.0
O24 A:7KK501 4.4 64.4 1.0
CD2 A:PHE363 4.6 71.8 1.0
OH A:TYR327 4.6 67.8 1.0
CZ A:PHE363 4.8 67.6 1.0
O A:HOH617 4.9 71.1 1.0
CE2 A:PHE363 5.0 74.0 1.0

Fluorine binding site 2 out of 4 in 5tto

Go back to Fluorine Binding Sites List in 5tto
Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Ppargamma in Complex with SR1643 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:70.5
occ:1.00
F32 A:7KK501 0.0 70.5 1.0
C28 A:7KK501 1.4 66.1 1.0
C29 A:7KK501 2.4 65.8 1.0
C27 A:7KK501 2.4 69.2 1.0
BR1 A:7KK501 3.1 87.2 1.0
CD2 A:LEU353 3.4 65.0 1.0
C22 A:7KK501 3.6 67.8 1.0
C26 A:7KK501 3.6 67.7 1.0
CG2 A:ILE281 3.8 65.6 1.0
CD2 A:LEU356 3.9 74.5 1.0
CG A:MET364 4.0 68.5 1.0
C25 A:7KK501 4.1 65.8 1.0
CG A:LEU353 4.4 58.8 1.0
O A:PHE360 4.4 78.3 1.0
CB A:LEU353 4.5 57.1 1.0
CB A:MET364 4.7 70.1 1.0
SG A:CYS285 4.7 67.8 1.0
CD1 A:LEU353 4.7 59.6 1.0
CB A:PHE363 4.8 66.5 1.0

Fluorine binding site 3 out of 4 in 5tto

Go back to Fluorine Binding Sites List in 5tto
Fluorine binding site 3 out of 4 in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Ppargamma in Complex with SR1643 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:70.2
occ:1.00
F30 B:7KK501 0.0 70.2 1.0
C25 B:7KK501 1.4 58.0 1.0
C26 B:7KK501 2.4 61.4 1.0
C22 B:7KK501 2.4 62.1 1.0
S21 B:7KK501 3.0 66.4 1.0
O23 B:7KK501 3.1 68.0 1.0
CE1 B:HIS449 3.2 66.7 1.0
N20 B:7KK501 3.3 53.2 1.0
CD1 B:PHE363 3.4 62.5 1.0
CG B:PHE363 3.6 61.6 1.0
C29 B:7KK501 3.6 65.2 1.0
C27 B:7KK501 3.6 73.2 1.0
CB B:PHE363 3.9 63.5 1.0
CE1 B:PHE363 4.0 68.3 1.0
NE2 B:HIS449 4.0 63.3 1.0
C28 B:7KK501 4.1 68.0 1.0
ND1 B:HIS449 4.3 64.9 1.0
CD2 B:PHE363 4.3 65.3 1.0
CD1 B:PHE282 4.3 68.4 1.0
CE1 B:PHE282 4.3 68.6 1.0
O B:HOH656 4.3 68.2 1.0
CB B:CYS285 4.4 55.1 1.0
OH B:TYR327 4.4 60.9 1.0
O24 B:7KK501 4.4 63.6 1.0
C15 B:7KK501 4.4 57.9 1.0
CZ B:PHE363 4.6 69.2 1.0
SG B:CYS285 4.6 60.2 1.0
CE2 B:PHE363 4.7 71.6 1.0

Fluorine binding site 4 out of 4 in 5tto

Go back to Fluorine Binding Sites List in 5tto
Fluorine binding site 4 out of 4 in the X-Ray Crystal Structure of Ppargamma in Complex with SR1643


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystal Structure of Ppargamma in Complex with SR1643 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:72.3
occ:1.00
F32 B:7KK501 0.0 72.3 1.0
C28 B:7KK501 1.4 68.0 1.0
C29 B:7KK501 2.4 65.2 1.0
C27 B:7KK501 2.4 73.2 1.0
BR1 B:7KK501 3.1 82.9 1.0
CD2 B:LEU353 3.3 68.7 1.0
C22 B:7KK501 3.6 62.1 1.0
C26 B:7KK501 3.6 61.4 1.0
CG2 B:ILE281 3.9 53.5 1.0
CE B:MET364 4.0 68.6 1.0
C25 B:7KK501 4.1 58.0 1.0
CD1 B:LEU356 4.3 78.0 1.0
CB B:MET364 4.5 60.9 1.0
CG B:LEU353 4.5 69.8 1.0
O B:PHE360 4.5 78.4 1.0
SG B:CYS285 4.5 60.2 1.0
CB B:LEU353 4.6 63.8 1.0
CB B:PHE363 4.9 63.5 1.0
CD1 B:LEU353 4.9 60.4 1.0
CB B:ILE281 4.9 63.9 1.0

Reference:

R.L.Frkic, Y.He, B.B.Rodriguez, M.R.Chang, D.Kuruvilla, A.Ciesla, A.D.Abell, T.M.Kamenecka, P.R.Griffin, J.B.Bruning. Structure-Activity Relationship of 2,4-Dichloro-N-(3,5-Dichloro-4-(Quinolin-3-Yloxy)Phenyl) Benzenesulfonamide (INT131) Analogs For Ppar Gamma-Targeted Antidiabetics. J. Med. Chem. V. 60 4584 2017.
ISSN: ISSN 1520-4804
PubMed: 28485590
DOI: 10.1021/ACS.JMEDCHEM.6B01727
Page generated: Sun Dec 13 12:38:30 2020

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