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Fluorine in PDB 6br2: Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist.

Protein crystallography data

The structure of Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist., PDB code: 6br2 was solved by R.J.Skene, I.Hoffman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.23 / 3.18
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 99.842, 99.842, 125.484, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 22.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist. (pdb code 6br2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist., PDB code: 6br2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6br2

Go back to Fluorine Binding Sites List in 6br2
Fluorine binding site 1 out of 2 in the Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:88.0
occ:1.00
F31 A:E3S502 0.0 88.0 1.0
C30 A:E3S502 1.4 81.3 1.0
C32 A:E3S502 2.3 79.3 1.0
C29 A:E3S502 2.4 77.0 1.0
C33 A:E3S502 3.0 77.0 1.0
C36 A:E3S502 3.1 72.2 1.0
C35 A:E3S502 3.1 81.8 1.0
CD2 A:LEU324 3.4 78.3 1.0
SG A:CYS320 3.5 81.2 1.0
C26 A:E3S502 3.6 76.7 1.0
C28 A:E3S502 3.7 73.9 1.0
CD1 A:LEU324 3.7 81.0 1.0
CB A:CYS320 3.7 75.8 1.0
C27 A:E3S502 4.1 76.6 1.0
CG A:LEU324 4.2 84.1 1.0
CA A:CYS320 4.2 79.8 1.0
O A:CYS320 4.3 86.2 1.0
C34 A:E3S502 4.5 78.9 1.0
C A:CYS320 4.6 81.2 1.0
O24 A:E3S502 4.7 78.4 1.0
N25 A:E3S502 4.8 78.0 1.0

Fluorine binding site 2 out of 2 in 6br2

Go back to Fluorine Binding Sites List in 6br2
Fluorine binding site 2 out of 2 in the Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Rorgt in Complex with A Novel Isoquinoline Inverse Agonist. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:85.7
occ:1.00
F31 B:E3S502 0.0 85.7 1.0
C30 B:E3S502 1.4 81.5 1.0
C32 B:E3S502 2.3 76.6 1.0
C29 B:E3S502 2.4 81.0 1.0
C33 B:E3S502 3.0 78.8 1.0
C35 B:E3S502 3.1 75.8 1.0
C36 B:E3S502 3.1 74.4 1.0
CD1 B:LEU324 3.4 66.8 1.0
CD2 B:LEU324 3.4 69.5 1.0
SG B:CYS320 3.6 88.3 1.0
C26 B:E3S502 3.6 79.2 1.0
C28 B:E3S502 3.7 79.6 1.0
CB B:CYS320 3.7 74.4 1.0
CG B:LEU324 4.0 74.0 1.0
C27 B:E3S502 4.1 80.7 1.0
CA B:CYS320 4.2 76.9 1.0
O B:CYS320 4.4 77.1 1.0
C34 B:E3S502 4.5 79.7 1.0
C B:CYS320 4.6 76.8 1.0
O24 B:E3S502 4.7 82.0 1.0
N25 B:E3S502 4.8 82.3 1.0

Reference:

M.Kono, A.Ochida, T.Oda, T.Imada, Y.Banno, N.Taya, S.Masada, T.Kawamoto, K.Yonemori, Y.Nara, Y.Fukase, T.Yukawa, H.Tokuhara, R.Skene, B.C.Sang, I.D.Hoffman, G.P.Snell, K.Uga, A.Shibata, K.Igaki, Y.Nakamura, H.Nakagawa, N.Tsuchimori, M.Yamasaki, J.Shirai, S.Yamamoto. Discovery of [ Cis-3-({(5 R)-5-[(7-Fluoro-1,1-Dimethyl-2,3-Dihydro-1 H-Inden-5-Yl)Carbamoyl]-2-Methoxy-7,8-Dihydro-1, 6-Naphthyridin-6(5 H)-Yl}Carbonyl)Cyclobutyl]Acetic Acid (Tak-828F) As A Potent, Selective, and Orally Available Novel Retinoic Acid Receptor-Related Orphan Receptor Gamma T Inverse Agonist. J. Med. Chem. V. 61 2973 2018.
ISSN: ISSN 1520-4804
PubMed: 29510038
DOI: 10.1021/ACS.JMEDCHEM.8B00061
Page generated: Tue Jul 15 10:12:46 2025

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