Fluorine in PDB 8b93: Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)

Protein crystallography data

The structure of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B), PDB code: 8b93 was solved by A.Friberg, D.L.Orsi, E.Pook, S.Siegel, C.T.Lemke, T.Stellfeld, V.Puetter, J.Goldstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.53 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.979, 85.479, 121.588, 90, 90, 90
R / Rfree (%) 27.3 / 38.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) (pdb code 8b93). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B), PDB code: 8b93:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 8b93

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Fluorine binding site 1 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:55.6
occ:1.00
 F37 A:Q8F501 0.0 55.6 1.0
C35 A:Q8F501 1.3 50.9 1.0
F36 A:Q8F501 2.2 50.4 1.0
F38 A:Q8F501 2.2 50.5 1.0
C32 A:Q8F501 2.3 43.2 1.0
C33 A:Q8F501 3.1 44.8 1.0
C31 A:Q8F501 3.3 43.2 1.0
CD1 A:LEU333 3.6 34.2 1.0
N A:LEU330 3.7 37.5 1.0
CB A:MET329 3.8 48.8 1.0
CD2 A:LEU330 3.8 35.0 1.0
C A:MET329 3.9 41.0 1.0
CG A:LEU330 3.9 36.9 1.0
CA A:LEU330 4.0 35.6 1.0
O A:MET329 4.2 41.1 1.0
C34 A:Q8F501 4.4 44.8 1.0
CE A:MET329 4.4 73.3 1.0
O A:ILE326 4.5 35.2 1.0
CA A:MET329 4.5 43.2 1.0
C29 A:Q8F501 4.5 43.6 1.0
CB A:LEU330 4.5 35.0 1.0
CG A:LEU333 4.6 34.8 1.0
O A:HOH629 4.8 29.6 1.0
NH1 A:ARG288 4.9 46.2 1.0
CG A:MET329 5.0 58.2 1.0

Fluorine binding site 2 out of 10 in 8b93

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Fluorine binding site 2 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:50.5
occ:1.00
 F38 A:Q8F501 0.0 50.5 1.0
C35 A:Q8F501 1.3 50.9 1.0
F36 A:Q8F501 2.1 50.4 1.0
F37 A:Q8F501 2.2 55.6 1.0
C32 A:Q8F501 2.3 43.2 1.0
C31 A:Q8F501 2.6 43.2 1.0
CD1 A:LEU333 3.1 34.2 1.0
O A:HOH629 3.2 29.6 1.0
NH1 A:ARG288 3.6 46.2 1.0
CZ A:ARG288 3.6 42.5 1.0
C33 A:Q8F501 3.7 44.8 1.0
NE A:ARG288 3.9 43.9 1.0
C29 A:Q8F501 4.0 43.6 1.0
NH2 A:ARG288 4.1 45.6 1.0
CG A:ARG288 4.1 41.0 1.0
CG A:LEU333 4.5 34.8 1.0
CD2 A:LEU330 4.5 35.0 1.0
CD A:ARG288 4.7 40.9 1.0
C34 A:Q8F501 4.8 44.8 1.0
O A:HOH637 4.8 37.5 1.0
C30 A:Q8F501 4.9 42.0 1.0
C28 A:Q8F501 5.0 44.9 1.0

Fluorine binding site 3 out of 10 in 8b93

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Fluorine binding site 3 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:50.4
occ:1.00
 F36 A:Q8F501 0.0 50.4 1.0
C35 A:Q8F501 1.3 50.9 1.0
F38 A:Q8F501 2.1 50.5 1.0
F37 A:Q8F501 2.2 55.6 1.0
C32 A:Q8F501 2.4 43.2 1.0
NH2 A:ARG288 3.0 45.6 1.0
NH1 A:ARG288 3.0 46.2 1.0
C33 A:Q8F501 3.1 44.8 1.0
CZ A:ARG288 3.1 42.5 1.0
C31 A:Q8F501 3.5 43.2 1.0
NE A:ARG288 4.1 43.9 1.0
CB A:ALA292 4.1 44.9 1.0
CE A:MET329 4.1 73.3 1.0
C34 A:Q8F501 4.4 44.8 1.0
CG A:ARG288 4.5 41.0 1.0
CD1 A:LEU333 4.6 34.2 1.0
CB A:MET329 4.6 48.8 1.0
OE1 A:GLU295 4.7 42.0 1.0
SD A:MET329 4.7 75.7 1.0
C29 A:Q8F501 4.8 43.6 1.0
CD A:ARG288 4.9 40.9 1.0
CA A:ALA292 5.0 49.6 1.0

Fluorine binding site 4 out of 10 in 8b93

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Fluorine binding site 4 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:42.6
occ:1.00
 F24 A:Q8F501 0.0 42.6 1.0
C5 A:Q8F501 1.3 48.7 1.0
OE1 A:GLN286 2.3 60.8 1.0
C4 A:Q8F501 2.3 45.5 1.0
C6 A:Q8F501 2.4 51.4 1.0
CZ A:PHE282 2.7 36.1 1.0
N8 A:Q8F501 3.0 52.9 1.0
C7 A:Q8F501 3.0 55.2 1.0
CE1 A:PHE282 3.2 36.4 1.0
CE2 A:PHE282 3.3 38.0 1.0
CD A:GLN286 3.5 62.4 1.0
C3 A:Q8F501 3.6 43.4 1.0
C1 A:Q8F501 3.6 45.5 1.0
CD1 A:LEU453 3.7 54.9 1.0
C2 A:Q8F501 4.1 42.8 1.0
O23 A:Q8F501 4.1 64.2 1.0
CD1 A:PHE282 4.1 37.4 1.0
CZ A:PHE363 4.2 54.7 1.0
CD2 A:PHE282 4.2 37.8 1.0
CA A:GLN286 4.2 44.5 1.0
NE2 A:GLN286 4.2 69.3 1.0
C9 A:Q8F501 4.3 60.2 1.0
CB A:GLN286 4.3 51.0 1.0
CG A:GLN286 4.5 53.8 1.0
N A:GLN286 4.5 43.5 1.0
O A:PHE282 4.6 46.7 1.0
CE1 A:PHE363 4.6 53.7 1.0
CG A:PHE282 4.6 40.1 1.0
CD2 A:LEU453 4.6 53.8 1.0
CG A:LEU453 4.8 56.6 1.0
SG A:CYS285 4.9 44.3 1.0
CE2 A:PHE363 4.9 54.5 1.0
C A:CYS285 5.0 46.4 1.0

Fluorine binding site 5 out of 10 in 8b93

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Fluorine binding site 5 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:76.6
occ:1.00
 F16 A:Q8F501 0.0 76.6 1.0
C13 A:Q8F501 1.3 73.7 1.0
C14 A:Q8F501 2.3 65.6 1.0
C12 A:Q8F501 2.4 70.9 1.0
CD1 C:ILE2353 3.4 47.3 1.0
C15 A:Q8F501 3.6 67.1 1.0
C11 A:Q8F501 3.7 65.0 1.0
CG2 A:VAL290 3.8 38.8 1.0
CD1 C:LEU2350 3.8 56.7 1.0
CA A:VAL290 3.9 42.0 1.0
C10 A:Q8F501 4.1 64.6 1.0
CG2 A:VAL293 4.1 54.0 1.0
CB A:VAL290 4.2 40.0 1.0
CB A:VAL293 4.4 50.5 1.0
O C:GLY2349 4.4 60.3 1.0
N A:VAL290 4.5 44.5 1.0
CG1 A:VAL293 4.5 53.3 1.0
CG1 C:ILE2353 4.6 50.2 1.0
CG1 A:VAL290 4.6 34.2 1.0
CB C:ILE2353 4.6 51.1 1.0
CG2 C:ILE2353 4.6 49.4 1.0
CA C:LEU2350 4.7 58.4 1.0
O A:SER289 4.8 32.5 1.0
C A:SER289 4.9 40.2 1.0
C17 A:Q8F501 4.9 68.4 1.0
O A:VAL290 4.9 46.0 1.0
C A:VAL290 5.0 44.1 1.0
C C:GLY2349 5.0 62.0 1.0

Fluorine binding site 6 out of 10 in 8b93

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Fluorine binding site 6 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:58.3
occ:1.00
 F37 B:Q8F501 0.0 58.3 1.0
C35 B:Q8F501 1.3 59.6 1.0
F36 B:Q8F501 2.1 48.1 1.0
F38 B:Q8F501 2.2 50.4 1.0
C32 B:Q8F501 2.4 58.2 1.0
C33 B:Q8F501 2.9 57.8 1.0
C31 B:Q8F501 3.5 57.0 1.0
N B:LEU330 3.7 36.5 1.0
CA B:LEU330 3.7 36.4 1.0
CD1 B:LEU330 3.8 39.8 1.0
CB B:LEU330 4.0 36.5 1.0
CB B:MET329 4.0 47.4 1.0
C B:MET329 4.1 37.1 1.0
O B:ILE326 4.2 34.6 1.0
C34 B:Q8F501 4.2 55.0 1.0
CD2 B:LEU333 4.2 36.1 1.0
O B:MET329 4.5 32.3 1.0
CG B:LEU330 4.5 35.4 1.0
C29 B:Q8F501 4.7 61.6 1.0
CA B:MET329 4.7 41.3 1.0
CG B:MET329 5.0 54.4 1.0
C28 B:Q8F501 5.0 51.7 1.0

Fluorine binding site 7 out of 10 in 8b93

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Fluorine binding site 7 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:50.4
occ:1.00
 F38 B:Q8F501 0.0 50.4 1.0
C35 B:Q8F501 1.3 59.6 1.0
F37 B:Q8F501 2.2 58.3 1.0
F36 B:Q8F501 2.2 48.1 1.0
C32 B:Q8F501 2.3 58.2 1.0
C31 B:Q8F501 2.7 57.0 1.0
CD2 B:LEU333 3.1 36.1 1.0
C33 B:Q8F501 3.6 57.8 1.0
NH1 B:ARG288 3.9 57.3 1.0
NE B:ARG288 4.0 60.1 1.0
CD1 B:LEU330 4.1 39.8 1.0
C29 B:Q8F501 4.1 61.6 1.0
CZ B:ARG288 4.2 61.9 1.0
CG B:LEU333 4.6 34.6 1.0
C34 B:Q8F501 4.7 55.0 1.0
CG B:ARG288 4.8 61.5 1.0
CD B:ARG288 4.9 64.0 1.0

Fluorine binding site 8 out of 10 in 8b93

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Fluorine binding site 8 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:48.1
occ:1.00
 F36 B:Q8F501 0.0 48.1 1.0
C35 B:Q8F501 1.3 59.6 1.0
F37 B:Q8F501 2.1 58.3 1.0
F38 B:Q8F501 2.2 50.4 1.0
C32 B:Q8F501 2.3 58.2 1.0
C33 B:Q8F501 2.9 57.8 1.0
NH1 B:ARG288 3.2 57.3 1.0
C31 B:Q8F501 3.4 57.0 1.0
CZ B:ARG288 3.5 61.9 1.0
NE B:ARG288 3.9 60.1 1.0
CB B:ALA292 4.0 45.9 1.0
NH2 B:ARG288 4.0 60.5 1.0
C34 B:Q8F501 4.1 55.0 1.0
C29 B:Q8F501 4.6 61.6 1.0
CG B:ARG288 4.8 61.5 1.0
OE1 B:GLU295 4.9 44.5 1.0
C28 B:Q8F501 4.9 51.7 1.0
CD B:ARG288 4.9 64.0 1.0
CA B:ALA292 4.9 47.7 1.0

Fluorine binding site 9 out of 10 in 8b93

Go back to Fluorine Binding Sites List in 8b93
Fluorine binding site 9 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:49.8
occ:1.00
 F24 B:Q8F501 0.0 49.8 1.0
C5 B:Q8F501 1.4 51.5 1.0
OE1 B:GLN286 2.3 60.4 1.0
C6 B:Q8F501 2.3 46.7 1.0
C4 B:Q8F501 2.5 51.3 1.0
N8 B:Q8F501 2.7 35.0 1.0
C7 B:Q8F501 2.8 39.1 1.0
CD B:GLN286 3.3 56.3 1.0
CE2 B:PHE282 3.3 49.5 1.0
CZ B:PHE282 3.4 51.4 1.0
CD1 B:LEU453 3.6 51.9 1.0
C1 B:Q8F501 3.6 45.3 1.0
C3 B:Q8F501 3.8 47.7 1.0
O23 B:Q8F501 3.9 37.8 1.0
C9 B:Q8F501 3.9 36.7 1.0
CZ B:PHE363 3.9 59.6 1.0
CB B:GLN286 3.9 52.3 1.0
NE2 B:GLN286 4.0 62.9 1.0
CA B:GLN286 4.1 51.3 1.0
CD2 B:PHE282 4.2 49.5 1.0
CG B:GLN286 4.2 53.3 1.0
C2 B:Q8F501 4.2 42.6 1.0
CE1 B:PHE282 4.3 52.4 1.0
CE2 B:PHE363 4.4 59.2 1.0
N B:GLN286 4.5 48.3 1.0
CG B:LEU453 4.6 53.5 1.0
O B:PHE282 4.9 41.9 1.0
CD2 B:LEU453 4.9 53.4 1.0
CE1 B:PHE363 4.9 58.6 1.0
CG B:PHE282 4.9 46.6 1.0
CD1 B:PHE282 5.0 49.5 1.0

Fluorine binding site 10 out of 10 in 8b93

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Fluorine binding site 10 out of 10 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound 15B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:43.3
occ:1.00
 F16 B:Q8F501 0.0 43.3 1.0
C13 B:Q8F501 1.3 47.2 1.0
C14 B:Q8F501 2.4 43.3 1.0
C12 B:Q8F501 2.4 47.9 1.0
CD1 D:ILE2353 2.9 45.2 1.0
CD1 D:LEU2350 3.3 58.5 1.0
CG2 B:VAL293 3.5 42.5 1.0
C15 B:Q8F501 3.6 36.9 1.0
C11 B:Q8F501 3.7 44.8 1.0
CB B:VAL293 4.1 43.6 1.0
CG1 D:ILE2353 4.1 44.1 1.0
CA D:LEU2350 4.1 59.6 1.0
C10 B:Q8F501 4.2 39.0 1.0
CG1 B:VAL293 4.2 41.8 1.0
CB D:LEU2350 4.2 57.2 1.0
CB D:ILE2353 4.3 45.4 1.0
CG D:LEU2350 4.4 54.6 1.0
CA B:VAL290 4.4 44.8 1.0
CG2 B:VAL290 4.4 44.0 1.0
CG2 D:ILE2353 4.6 44.7 1.0
CB B:VAL290 4.8 41.7 1.0
O D:LEU2350 4.9 56.5 1.0
C17 B:Q8F501 5.0 44.1 1.0
CG1 B:VAL290 5.0 41.7 1.0

Reference:

D.L.Orsi, S.J.Ferrara, S.Siegel, A.Friberg, L.Bouche, E.Pook, P.Lienau, J.P.Bluck, C.T.Lemke, G.Akcay, T.Stellfeld, H.Meyer, V.Putter, S.J.Holton, D.Korr, I.Jerchel-Furau, C.Pantelidou, C.A.Strathdee, M.Meyerson, K.Eis, J.T.Goldstein. Discovery and Characterization of Orally Bioavailable 4-Chloro-6-Fluoroisophthalamides As Covalent Pparg Inverse-Agonists. Bioorg.Med.Chem. V. 78 17130 2022.
ISSN: ESSN 1464-3391
PubMed: 36542958
DOI: 10.1016/J.BMC.2022.117130
Page generated: Wed Apr 5 02:05:11 2023

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