Fluorine in PDB 5yp6: Rorgamma (263-509) Complexed with SRC2 and Compound 6

Protein crystallography data

The structure of Rorgamma (263-509) Complexed with SRC2 and Compound 6, PDB code: 5yp6 was solved by M.Gao, W.Cai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.72 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.201, 62.201, 154.822, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Rorgamma (263-509) Complexed with SRC2 and Compound 6 (pdb code 5yp6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Rorgamma (263-509) Complexed with SRC2 and Compound 6, PDB code: 5yp6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5yp6

Go back to Fluorine Binding Sites List in 5yp6
Fluorine binding site 1 out of 3 in the Rorgamma (263-509) Complexed with SRC2 and Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rorgamma (263-509) Complexed with SRC2 and Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:27.0
occ:1.00
F2 A:4CX601 0.0 27.0 1.0
C26 A:4CX601 1.3 26.9 1.0
F1 A:4CX601 2.2 27.6 1.0
F3 A:4CX601 2.2 26.9 1.0
C24 A:4CX601 2.3 26.4 1.0
C12 A:4CX601 3.0 26.4 1.0
C13 A:4CX601 3.1 25.9 1.0
C22 A:4CX601 3.1 26.3 1.0
C25 A:4CX601 3.4 26.5 1.0
CG2 A:ILE400 3.5 18.6 1.0
C14 A:4CX601 4.0 26.1 1.0
C21 A:4CX601 4.1 26.4 1.0
CG A:MET365 4.2 19.7 1.0
CD1 A:ILE400 4.3 18.8 1.0
C11 A:4CX601 4.3 26.3 1.0
CE A:MET365 4.4 23.0 1.0
C9 A:4CX601 4.6 26.4 1.0
SD A:MET365 4.6 23.5 1.0
CB A:ILE400 4.6 18.7 1.0
C23 A:4CX601 4.8 26.5 1.0
C15 A:4CX601 4.8 26.4 1.0
C16 A:4CX601 4.8 26.3 1.0
CG1 A:ILE400 4.9 18.8 1.0
C10 A:4CX601 5.0 26.5 1.0

Fluorine binding site 2 out of 3 in 5yp6

Go back to Fluorine Binding Sites List in 5yp6
Fluorine binding site 2 out of 3 in the Rorgamma (263-509) Complexed with SRC2 and Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rorgamma (263-509) Complexed with SRC2 and Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:26.9
occ:1.00
F3 A:4CX601 0.0 26.9 1.0
C26 A:4CX601 1.3 26.9 1.0
F1 A:4CX601 2.2 27.6 1.0
F2 A:4CX601 2.2 27.0 1.0
C24 A:4CX601 2.4 26.4 1.0
C13 A:4CX601 2.9 25.9 1.0
C12 A:4CX601 3.0 26.4 1.0
C14 A:4CX601 3.1 26.1 1.0
C25 A:4CX601 3.5 26.5 1.0
CZ A:PHE388 3.6 18.5 1.0
C22 A:4CX601 3.7 26.3 1.0
CE1 A:PHE388 3.9 18.8 1.0
C15 A:4CX601 3.9 26.4 1.0
CE2 A:PHE388 4.0 18.5 1.0
C11 A:4CX601 4.3 26.3 1.0
CE1 A:PHE401 4.4 18.9 1.0
C21 A:4CX601 4.4 26.4 1.0
CG1 A:VAL376 4.5 18.4 1.0
C16 A:4CX601 4.5 26.3 1.0
CD1 A:PHE388 4.5 18.6 1.0
CD2 A:PHE388 4.6 18.7 1.0
CD1 A:ILE397 4.6 20.4 1.0
CG2 A:ILE400 4.6 18.6 1.0
C9 A:4CX601 4.7 26.4 1.0
CG A:PHE388 4.8 19.0 1.0
C10 A:4CX601 5.0 26.5 1.0

Fluorine binding site 3 out of 3 in 5yp6

Go back to Fluorine Binding Sites List in 5yp6
Fluorine binding site 3 out of 3 in the Rorgamma (263-509) Complexed with SRC2 and Compound 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rorgamma (263-509) Complexed with SRC2 and Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:27.6
occ:1.00
F1 A:4CX601 0.0 27.6 1.0
C26 A:4CX601 1.3 26.9 1.0
F2 A:4CX601 2.2 27.0 1.0
F3 A:4CX601 2.2 26.9 1.0
C24 A:4CX601 2.4 26.4 1.0
C25 A:4CX601 2.7 26.5 1.0
CG2 A:VAL376 3.2 18.8 1.0
CG1 A:VAL376 3.4 18.4 1.0
C12 A:4CX601 3.7 26.4 1.0
CB A:VAL376 3.7 18.8 1.0
CG A:MET365 4.0 19.7 1.0
C9 A:4CX601 4.1 26.4 1.0
SD A:MET365 4.1 23.5 1.0
C13 A:4CX601 4.3 25.9 1.0
CE1 A:PHE401 4.5 18.9 1.0
CG2 A:ILE400 4.6 18.6 1.0
CZ A:PHE388 4.6 18.5 1.0
CE A:MET365 4.7 23.0 1.0
C11 A:4CX601 4.8 26.3 1.0
N1 A:4CX601 4.8 26.4 1.0
C22 A:4CX601 4.9 26.3 1.0
C14 A:4CX601 4.9 26.1 1.0
CE1 A:PHE388 4.9 18.8 1.0
C10 A:4CX601 5.0 26.5 1.0

Reference:

Y.Wang, W.Cai, T.Tang, Q.Liu, T.Yang, L.Yang, Y.Ma, G.Zhang, Y.Huang, X.Song, L.A.Orband-Miller, Q.Wu, L.Zhou, Z.Xiang, J.N.Xiang, S.Leung, L.Shao, X.Lin, M.Lobera, F.Ren. From Ror Gamma T Agonist to Two Types of Ror Gamma T Inverse Agonists Acs Med Chem Lett V. 9 120 2018.
ISSN: ISSN 1948-5875
PubMed: 29456799
DOI: 10.1021/ACSMEDCHEMLETT.7B00476
Page generated: Sun Dec 13 12:43:31 2020

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