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Fluorine in PDB 5apj: Ligand Complex of Rorg Lbd

Protein crystallography data

The structure of Ligand Complex of Rorg Lbd, PDB code: 5apj was solved by Y.Xue, A.Aagaard, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 2.08
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.950, 61.950, 159.600, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 5apj:

The structure of Ligand Complex of Rorg Lbd also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ligand Complex of Rorg Lbd (pdb code 5apj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ligand Complex of Rorg Lbd, PDB code: 5apj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5apj

Go back to Fluorine Binding Sites List in 5apj
Fluorine binding site 1 out of 4 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ligand Complex of Rorg Lbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1508

b:66.5
occ:1.00
F30 A:76E1508 0.0 66.5 1.0
C16 A:76E1508 1.3 63.9 1.0
C11 A:76E1508 2.3 64.1 1.0
C6 A:76E1508 2.4 63.6 1.0
C19 A:76E1508 2.7 62.6 1.0
CD1 A:ILE397 3.1 37.9 1.0
O26 A:76E1508 3.2 61.6 1.0
F31 A:76E1508 3.2 55.2 1.0
F32 A:76E1508 3.2 55.2 1.0
CD1 A:ILE400 3.3 25.3 1.0
N25 A:76E1508 3.4 59.5 1.0
C2 A:76E1508 3.6 65.0 1.0
C18 A:76E1508 3.6 64.7 1.0
C23 A:76E1508 3.8 54.4 1.0
C8 A:76E1508 4.1 64.9 1.0
F33 A:76E1508 4.2 56.6 1.0
CD2 A:LEU396 4.3 31.5 1.0
C14 A:76E1508 4.3 59.2 1.0
CG A:LEU396 4.4 29.2 1.0
CG1 A:ILE397 4.4 30.1 1.0
CD1 A:LEU391 4.7 26.3 1.0
C4 A:76E1508 4.7 58.9 1.0
CG1 A:ILE400 4.7 26.0 1.0

Fluorine binding site 2 out of 4 in 5apj

Go back to Fluorine Binding Sites List in 5apj
Fluorine binding site 2 out of 4 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ligand Complex of Rorg Lbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1508

b:55.2
occ:1.00
F31 A:76E1508 0.0 55.2 1.0
C23 A:76E1508 1.4 54.4 1.0
F32 A:76E1508 2.2 55.2 1.0
F33 A:76E1508 2.2 56.6 1.0
C13 A:76E1508 2.4 51.9 1.0
O26 A:76E1508 2.7 61.6 1.0
C10 A:76E1508 2.9 50.4 1.0
F30 A:76E1508 3.2 66.5 1.0
C19 A:76E1508 3.5 62.6 1.0
CD1 A:ILE397 3.5 37.9 1.0
CD1 A:PHE388 3.6 28.2 1.0
C3 A:76E1508 3.6 50.6 1.0
CE1 A:PHE388 3.7 31.2 1.0
C16 A:76E1508 3.9 63.9 1.0
CG A:PHE388 4.0 27.2 1.0
C11 A:76E1508 4.0 64.1 1.0
CZ A:PHE388 4.2 29.8 1.0
C17 A:76E1508 4.2 53.2 1.0
N25 A:76E1508 4.4 59.5 1.0
CD1 A:LEU391 4.4 26.3 1.0
CD2 A:PHE388 4.5 29.1 1.0
C14 A:76E1508 4.6 59.2 1.0
CE2 A:PHE388 4.6 30.6 1.0
SG A:CYS320 4.7 28.1 1.0
CB A:PHE388 4.7 27.2 1.0
C1 A:76E1508 4.7 49.1 1.0
C9 A:76E1508 4.8 58.6 1.0
CG1 A:ILE397 4.9 30.1 1.0
C6 A:76E1508 5.0 63.6 1.0
C7 A:76E1508 5.0 49.6 1.0

Fluorine binding site 3 out of 4 in 5apj

Go back to Fluorine Binding Sites List in 5apj
Fluorine binding site 3 out of 4 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ligand Complex of Rorg Lbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1508

b:55.2
occ:1.00
F32 A:76E1508 0.0 55.2 1.0
C23 A:76E1508 1.4 54.4 1.0
F31 A:76E1508 2.2 55.2 1.0
F33 A:76E1508 2.2 56.6 1.0
C13 A:76E1508 2.3 51.9 1.0
C10 A:76E1508 3.1 50.4 1.0
F30 A:76E1508 3.2 66.5 1.0
C3 A:76E1508 3.2 50.6 1.0
O26 A:76E1508 3.3 61.6 1.0
C4 A:76E1508 3.5 58.9 1.0
C19 A:76E1508 3.6 62.6 1.0
C14 A:76E1508 3.6 59.2 1.0
CD1 A:ILE400 3.6 25.3 1.0
N25 A:76E1508 3.8 59.5 1.0
CG2 A:ILE400 3.9 25.5 1.0
C5 A:76E1508 4.0 58.9 1.0
C9 A:76E1508 4.2 58.6 1.0
C16 A:76E1508 4.3 63.9 1.0
C17 A:76E1508 4.3 53.2 1.0
C11 A:76E1508 4.4 64.1 1.0
C1 A:76E1508 4.4 49.1 1.0
SD A:MET365 4.5 44.6 1.0
CD1 A:ILE397 4.5 37.9 1.0
CB A:ILE400 4.5 26.6 1.0
C15 A:76E1508 4.6 57.9 1.0
CG1 A:ILE400 4.6 26.0 1.0
CE A:MET365 4.7 40.8 1.0
C12 A:76E1508 4.7 58.0 1.0
C7 A:76E1508 4.9 49.6 1.0

Fluorine binding site 4 out of 4 in 5apj

Go back to Fluorine Binding Sites List in 5apj
Fluorine binding site 4 out of 4 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ligand Complex of Rorg Lbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1508

b:56.6
occ:1.00
F33 A:76E1508 0.0 56.6 1.0
C23 A:76E1508 1.4 54.4 1.0
F31 A:76E1508 2.2 55.2 1.0
F32 A:76E1508 2.2 55.2 1.0
C13 A:76E1508 2.4 51.9 1.0
C3 A:76E1508 2.8 50.6 1.0
C10 A:76E1508 3.6 50.4 1.0
CE1 A:PHE401 3.7 29.8 1.0
CD1 A:ILE397 3.8 37.9 1.0
CE2 A:PHE388 4.0 30.6 1.0
CD2 A:PHE388 4.1 29.1 1.0
CZ A:PHE388 4.1 29.8 1.0
C1 A:76E1508 4.1 49.1 1.0
CG2 A:ILE397 4.1 29.2 1.0
CG A:PHE388 4.2 27.2 1.0
F30 A:76E1508 4.2 66.5 1.0
CD1 A:PHE401 4.3 29.4 1.0
CG2 A:ILE400 4.3 25.5 1.0
CE1 A:PHE388 4.3 31.2 1.0
CD1 A:PHE388 4.4 28.2 1.0
O26 A:76E1508 4.6 61.6 1.0
CD1 A:ILE400 4.7 25.3 1.0
CZ A:PHE401 4.7 28.3 1.0
CB A:ILE400 4.7 26.6 1.0
C17 A:76E1508 4.7 53.2 1.0
CB A:ILE397 4.8 29.9 1.0
CG1 A:ILE397 4.8 30.1 1.0
CA A:ILE397 4.9 26.6 1.0
C7 A:76E1508 5.0 49.6 1.0

Reference:

R.I.Olsson, Y.Xue, S.Von Berg, A.Aagaard, J.Mcpheat, E.L.Hansson, J.Bernstrom, P.Hansson, J.Jirholt, H.Grindebacke, A.Leffler, R.Chen, Y.Xiong, H.Ge, T.G.Hansson, F.Narjes. Benzoxazepines Achieve Potent Suppression of Il-17 Release in Human T-Helper 17 (Th 17) Cells Through An Induced-Fit Binding Mode to the Nuclear Receptor Ror Gamma. Chemmedchem V. 11 207 2016.
ISSN: ESSN 1860-7187
PubMed: 26553345
DOI: 10.1002/CMDC.201500432
Page generated: Thu Aug 1 07:49:56 2024

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