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Fluorine in PDB 7jym: Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist

Protein crystallography data

The structure of Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist, PDB code: 7jym was solved by J.Sack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.05 / 3.05
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.297, 61.297, 155.945, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist (pdb code 7jym). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist, PDB code: 7jym:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 7jym

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Fluorine binding site 1 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:51.4
occ:1.00
F26 A:Z8I4000 0.0 51.4 1.0
C14 A:Z8I4000 1.4 51.8 1.0
C25 A:Z8I4000 2.3 53.6 1.0
C24 A:Z8I4000 2.3 50.8 1.0
C11 A:Z8I4000 2.4 50.9 1.0
H57 A:Z8I4000 2.5 60.8 0.0
F27 A:Z8I4000 2.6 54.3 1.0
F31 A:Z8I4000 2.7 50.8 1.0
F30 A:Z8I4000 2.8 50.7 1.0
C10 A:Z8I4000 2.8 50.7 1.0
F28 A:Z8I4000 2.8 54.0 1.0
F29 A:Z8I4000 3.5 53.9 1.0
F32 A:Z8I4000 3.5 50.0 1.0
C12 A:Z8I4000 3.6 50.6 1.0
CD1 A:ILE400 3.8 28.1 1.0
CE A:MET358 3.8 26.9 1.0
CD2 A:HIS479 4.0 29.6 1.0
H58 A:Z8I4000 4.0 60.7 0.0
CD2 A:LEU396 4.1 38.7 1.0
C8 A:Z8I4000 4.2 50.5 1.0
CG A:HIS479 4.3 28.8 1.0
CG A:LEU396 4.5 38.7 1.0
NE2 A:HIS479 4.6 30.6 1.0
CB A:HIS479 4.6 26.9 1.0
H56 A:Z8I4000 4.7 60.5 0.0
CD1 A:LEU396 4.7 39.1 1.0
C13 A:Z8I4000 4.8 50.6 1.0
ND1 A:HIS479 5.0 30.6 1.0
CD2 A:LEU324 5.0 27.1 1.0

Fluorine binding site 2 out of 9 in 7jym

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Fluorine binding site 2 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:54.3
occ:1.00
F27 A:Z8I4000 0.0 54.3 1.0
C25 A:Z8I4000 1.3 53.6 1.0
F29 A:Z8I4000 2.2 53.9 1.0
F28 A:Z8I4000 2.2 54.0 1.0
C14 A:Z8I4000 2.4 51.8 1.0
F26 A:Z8I4000 2.6 51.4 1.0
F31 A:Z8I4000 2.6 50.8 1.0
CD2 A:HIS479 2.9 29.6 1.0
C24 A:Z8I4000 2.9 50.8 1.0
NE2 A:HIS479 3.3 30.6 1.0
F32 A:Z8I4000 3.5 50.0 1.0
C11 A:Z8I4000 3.7 50.9 1.0
CG A:HIS479 3.9 28.8 1.0
CH2 A:TRP317 3.9 30.9 1.0
CZ3 A:TRP317 4.0 30.6 1.0
H58 A:Z8I4000 4.0 60.7 0.0
CD2 A:LEU396 4.1 38.7 1.0
F30 A:Z8I4000 4.1 50.7 1.0
OH A:TYR502 4.2 31.4 1.0
C12 A:Z8I4000 4.3 50.6 1.0
CE1 A:HIS479 4.4 31.0 1.0
CB A:HIS479 4.7 26.9 1.0
ND1 A:HIS479 4.8 30.6 1.0
C10 A:Z8I4000 4.8 50.7 1.0
CZ2 A:TRP317 4.8 30.7 1.0
CA A:HIS479 4.8 26.1 1.0
H57 A:Z8I4000 4.9 60.8 0.0
CE3 A:TRP317 4.9 30.0 1.0
O A:HIS479 4.9 25.6 1.0

Fluorine binding site 3 out of 9 in 7jym

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Fluorine binding site 3 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:54.0
occ:1.00
F28 A:Z8I4000 0.0 54.0 1.0
C25 A:Z8I4000 1.3 53.6 1.0
F27 A:Z8I4000 2.2 54.3 1.0
F29 A:Z8I4000 2.2 53.9 1.0
C14 A:Z8I4000 2.4 51.8 1.0
F26 A:Z8I4000 2.8 51.4 1.0
H58 A:Z8I4000 2.8 60.7 0.0
C11 A:Z8I4000 2.9 50.9 1.0
C12 A:Z8I4000 3.1 50.6 1.0
NE2 A:HIS479 3.1 30.6 1.0
CD2 A:LEU324 3.2 27.1 1.0
CD2 A:HIS479 3.4 29.6 1.0
C24 A:Z8I4000 3.7 50.8 1.0
OH A:TYR502 3.9 31.4 1.0
CE1 A:HIS479 3.9 31.0 1.0
C10 A:Z8I4000 4.0 50.7 1.0
F31 A:Z8I4000 4.1 50.8 1.0
F32 A:Z8I4000 4.1 50.0 1.0
CE2 A:TYR502 4.2 28.4 1.0
C13 A:Z8I4000 4.3 50.6 1.0
CG A:HIS479 4.3 28.8 1.0
CG A:LEU324 4.3 26.6 1.0
H57 A:Z8I4000 4.4 60.8 0.0
CB A:LEU324 4.5 25.5 1.0
CZ A:TYR502 4.5 29.5 1.0
CE A:MET358 4.5 26.9 1.0
ND1 A:HIS479 4.6 30.6 1.0
F30 A:Z8I4000 4.8 50.7 1.0
H59 A:Z8I4000 4.8 60.8 0.0
C8 A:Z8I4000 5.0 50.5 1.0
CD1 A:LEU324 5.0 27.1 1.0

Fluorine binding site 4 out of 9 in 7jym

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Fluorine binding site 4 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:53.9
occ:1.00
F29 A:Z8I4000 0.0 53.9 1.0
C25 A:Z8I4000 1.3 53.6 1.0
F27 A:Z8I4000 2.2 54.3 1.0
F28 A:Z8I4000 2.2 54.0 1.0
H58 A:Z8I4000 2.3 60.7 0.0
C14 A:Z8I4000 2.4 51.8 1.0
F32 A:Z8I4000 2.6 50.0 1.0
C24 A:Z8I4000 2.9 50.8 1.0
C12 A:Z8I4000 3.0 50.6 1.0
C11 A:Z8I4000 3.1 50.9 1.0
F31 A:Z8I4000 3.3 50.8 1.0
F26 A:Z8I4000 3.5 51.4 1.0
CB A:CYS320 3.7 24.5 1.0
CZ3 A:TRP317 4.1 30.6 1.0
F30 A:Z8I4000 4.1 50.7 1.0
C13 A:Z8I4000 4.3 50.6 1.0
CE3 A:TRP317 4.4 30.0 1.0
C10 A:Z8I4000 4.4 50.7 1.0
CH2 A:TRP317 4.5 30.9 1.0
OH A:TYR502 4.5 31.4 1.0
H59 A:Z8I4000 4.6 60.8 0.0
C A:CYS320 4.6 25.2 1.0
NE2 A:HIS479 4.7 30.6 1.0
CD2 A:HIS479 4.7 29.6 1.0
N A:ALA321 4.7 24.7 1.0
CA A:CYS320 4.8 24.8 1.0
SG A:CYS320 4.9 25.7 1.0
H57 A:Z8I4000 5.0 60.8 0.0

Fluorine binding site 5 out of 9 in 7jym

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Fluorine binding site 5 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:50.7
occ:1.00
F30 A:Z8I4000 0.0 50.7 1.0
C24 A:Z8I4000 1.3 50.8 1.0
F32 A:Z8I4000 2.1 50.0 1.0
F31 A:Z8I4000 2.1 50.8 1.0
C14 A:Z8I4000 2.4 51.8 1.0
F26 A:Z8I4000 2.8 51.4 1.0
C11 A:Z8I4000 2.9 50.9 1.0
H57 A:Z8I4000 2.9 60.8 0.0
H62 A:Z8I4000 3.0 61.8 0.0
C10 A:Z8I4000 3.1 50.7 1.0
CD1 A:ILE397 3.2 38.1 1.0
CD1 A:ILE400 3.2 28.1 1.0
C19 A:Z8I4000 3.6 51.5 1.0
C25 A:Z8I4000 3.7 53.6 1.0
C12 A:Z8I4000 3.9 50.6 1.0
F29 A:Z8I4000 4.1 53.9 1.0
H63 A:Z8I4000 4.1 62.1 0.0
F27 A:Z8I4000 4.1 54.3 1.0
C20 A:Z8I4000 4.2 51.8 1.0
C8 A:Z8I4000 4.2 50.5 1.0
C21 A:Z8I4000 4.3 51.6 1.0
H58 A:Z8I4000 4.3 60.7 0.0
F33 A:Z8I4000 4.4 51.7 1.0
CG A:LEU396 4.4 38.7 1.0
CD2 A:LEU396 4.5 38.7 1.0
CG1 A:ILE397 4.5 36.8 1.0
CG1 A:ILE400 4.6 27.0 1.0
F28 A:Z8I4000 4.8 54.0 1.0
C13 A:Z8I4000 4.8 50.6 1.0
H55 A:Z8I4000 4.9 60.5 0.0
CD1 A:LEU391 4.9 31.1 1.0
C9 A:Z8I4000 4.9 50.9 1.0
C7 A:Z8I4000 5.0 50.4 1.0

Fluorine binding site 6 out of 9 in 7jym

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Fluorine binding site 6 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:50.8
occ:1.00
F31 A:Z8I4000 0.0 50.8 1.0
C24 A:Z8I4000 1.3 50.8 1.0
F32 A:Z8I4000 2.1 50.0 1.0
F30 A:Z8I4000 2.1 50.7 1.0
C14 A:Z8I4000 2.4 51.8 1.0
F27 A:Z8I4000 2.6 54.3 1.0
F26 A:Z8I4000 2.7 51.4 1.0
C25 A:Z8I4000 2.9 53.6 1.0
CD2 A:LEU396 3.1 38.7 1.0
F29 A:Z8I4000 3.3 53.9 1.0
C11 A:Z8I4000 3.7 50.9 1.0
CG A:LEU396 3.7 38.7 1.0
SG A:CYS393 3.9 48.5 1.0
F28 A:Z8I4000 4.1 54.0 1.0
CD1 A:ILE397 4.3 38.1 1.0
H57 A:Z8I4000 4.3 60.8 0.0
C10 A:Z8I4000 4.4 50.7 1.0
CB A:CYS393 4.5 43.6 1.0
C12 A:Z8I4000 4.6 50.6 1.0
H58 A:Z8I4000 4.6 60.7 0.0
CD1 A:ILE400 4.6 28.1 1.0
CB A:LEU396 4.7 38.2 1.0
H62 A:Z8I4000 4.7 61.8 0.0
CD1 A:LEU396 4.7 39.1 1.0
CD1 A:LEU391 4.8 31.1 1.0
CH2 A:TRP317 5.0 30.9 1.0

Fluorine binding site 7 out of 9 in 7jym

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Fluorine binding site 7 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:50.0
occ:1.00
F32 A:Z8I4000 0.0 50.0 1.0
C24 A:Z8I4000 1.3 50.8 1.0
F31 A:Z8I4000 2.1 50.8 1.0
F30 A:Z8I4000 2.1 50.7 1.0
C14 A:Z8I4000 2.4 51.8 1.0
F29 A:Z8I4000 2.6 53.9 1.0
C11 A:Z8I4000 2.9 50.9 1.0
C25 A:Z8I4000 2.9 53.6 1.0
H58 A:Z8I4000 3.2 60.7 0.0
C12 A:Z8I4000 3.3 50.6 1.0
H62 A:Z8I4000 3.4 61.8 0.0
CD1 A:LEU391 3.4 31.1 1.0
F26 A:Z8I4000 3.5 51.4 1.0
F27 A:Z8I4000 3.5 54.3 1.0
H63 A:Z8I4000 3.7 62.1 0.0
C10 A:Z8I4000 3.9 50.7 1.0
CD1 A:ILE397 4.0 38.1 1.0
C19 A:Z8I4000 4.1 51.5 1.0
F28 A:Z8I4000 4.1 54.0 1.0
CB A:CYS320 4.2 24.5 1.0
H57 A:Z8I4000 4.3 60.8 0.0
C20 A:Z8I4000 4.3 51.8 1.0
SG A:CYS320 4.3 25.7 1.0
C13 A:Z8I4000 4.4 50.6 1.0
CD2 A:LEU391 4.6 30.9 1.0
CG A:LEU391 4.6 30.8 1.0
C8 A:Z8I4000 4.9 50.5 1.0
H59 A:Z8I4000 4.9 60.8 0.0
SG A:CYS393 5.0 48.5 1.0

Fluorine binding site 8 out of 9 in 7jym

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Fluorine binding site 8 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:51.7
occ:1.00
F33 A:Z8I4000 0.0 51.7 1.0
C21 A:Z8I4000 1.4 51.6 1.0
C19 A:Z8I4000 2.3 51.5 1.0
C18 A:Z8I4000 2.3 51.7 1.0
H62 A:Z8I4000 2.6 61.8 0.0
H61 A:Z8I4000 2.6 62.0 0.0
CE1 A:PHE401 3.2 28.6 1.0
CD1 A:ILE397 3.4 38.1 1.0
C20 A:Z8I4000 3.6 51.8 1.0
C17 A:Z8I4000 3.6 51.9 1.0
CD1 A:PHE401 3.6 27.8 1.0
CD2 A:PHE388 3.8 28.7 1.0
CE2 A:PHE388 3.8 29.2 1.0
CG2 A:ILE400 3.8 26.6 1.0
CG2 A:ILE397 4.0 36.0 1.0
C16 A:Z8I4000 4.1 52.3 1.0
CZ A:PHE388 4.3 29.1 1.0
CG A:PHE388 4.3 28.2 1.0
F30 A:Z8I4000 4.4 50.7 1.0
CZ A:PHE401 4.4 28.6 1.0
H55 A:Z8I4000 4.4 60.5 0.0
CB A:ILE400 4.4 26.4 1.0
H60 A:Z8I4000 4.5 62.2 0.0
H63 A:Z8I4000 4.5 62.1 0.0
O A:ILE397 4.5 34.4 1.0
CG1 A:ILE397 4.5 36.8 1.0
CA A:ILE397 4.5 35.4 1.0
CB A:ILE397 4.6 35.7 1.0
CD1 A:ILE400 4.7 28.1 1.0
CD1 A:PHE388 4.8 29.0 1.0
CE1 A:PHE388 4.8 29.7 1.0
CG A:PHE401 5.0 27.2 1.0
C A:ILE397 5.0 34.5 1.0

Fluorine binding site 9 out of 9 in 7jym

Go back to Fluorine Binding Sites List in 7jym
Fluorine binding site 9 out of 9 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with A Tricyclic Sulfone Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:47.8
occ:1.00
F42 A:Z8I4000 0.0 47.8 1.0
C38 A:Z8I4000 1.4 47.5 1.0
H67 A:Z8I4000 2.0 57.0 0.0
C37 A:Z8I4000 2.4 47.5 1.0
C39 A:Z8I4000 2.4 47.4 1.0
H66 A:Z8I4000 2.5 56.9 0.0
O41 A:Z8I4000 2.9 47.2 1.0
H65 A:Z8I4000 2.9 56.9 0.0
CB A:ARG364 3.0 22.8 1.0
N40 A:Z8I4000 3.4 47.7 1.0
C35 A:Z8I4000 3.6 47.9 1.0
CG A:ARG364 3.6 25.0 1.0
CD A:ARG364 3.7 27.6 1.0
C A:ARG364 3.7 22.3 1.0
N A:MET365 3.9 22.1 1.0
CA A:ARG364 4.0 21.9 1.0
O A:ARG364 4.1 22.8 1.0
H64 A:Z8I4000 4.3 57.4 0.0
O A:VAL361 4.3 21.2 1.0
CA A:MET365 4.4 22.8 1.0
H73 A:Z8I4000 4.4 56.9 0.0
C34 A:Z8I4000 4.6 48.6 1.0
CA A:VAL361 4.6 22.5 1.0
CG1 A:VAL361 4.7 23.1 1.0
NH1 A:ARG364 4.7 31.5 1.0
C43 A:Z8I4000 4.8 47.9 1.0
NE A:ARG364 4.9 30.1 1.0
C A:VAL361 4.9 22.0 1.0
O36 A:Z8I4000 4.9 48.4 1.0
H68 A:Z8I4000 5.0 57.4 0.0
N A:ARG364 5.0 22.1 1.0
CB A:MET365 5.0 24.2 1.0

Reference:

Q.Shi, Z.Xiao, M.G.Yang, D.Marcoux, R.J.Cherney, L.A.M.Cornelius, S.Yip, D.R.Wu, C.A.Weigelt, J.Sack, J.Khan, M.Ruzanov, J.Wang, M.Yarde, M.E.Cvijic, S.Li, D.J.Shuster, V.Borowski, J.Xie, T.Sherry, M.Obermeier, A.Fura, K.Stefanski, G.Cornelius, S.Chacko, J.Hynes, J.A.Tino, J.E.Macor, L.Salter-Cid, R.Denton, Q.Zhao, T.G.M.Dhar. Novel Tricyclic Pyroglutamide Derivatives As Potent Rorgt Inverse Agonists Identified Using A Virtual Screening Approach Acs Med.Chem.Lett. 2020.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.0C00496
Page generated: Tue Jul 15 20:40:19 2025

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