Fluorine in PDB 5z5s: Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB

Protein crystallography data

The structure of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB, PDB code: 5z5s was solved by Y.Matsui, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.408, 54.015, 66.242, 90.00, 106.48, 90.00
R / Rfree (%) n/a / n/a

Other elements in 5z5s:

The structure of Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB (pdb code 5z5s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB, PDB code: 5z5s:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5z5s

Go back to Fluorine Binding Sites List in 5z5s
Fluorine binding site 1 out of 2 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


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 the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:33.4
occ:0.50
F9 A:RTE501 0.0 33.4 0.5
C2 A:RTE501 1.3 33.1 0.5
C6 A:RTE501 1.4 30.8 0.5
C1 A:RTE501 2.1 31.5 0.5
C3 A:RTE501 2.3 32.0 0.5
C1 A:RTE501 2.4 33.2 0.5
C5 A:RTE501 2.5 30.3 0.5
CL1 A:RTE501 2.6 34.6 0.5
CL1 A:RTE501 2.9 37.0 0.5
C2 A:RTE501 3.3 31.8 0.5
NH2 A:ARG280 3.5 38.2 1.0
C4 A:RTE501 3.6 29.7 0.5
C4 A:RTE501 3.6 31.1 0.5
C6 A:RTE501 3.6 33.4 0.5
C3 A:RTE501 3.9 30.8 0.5
CG A:GLU259 4.0 43.3 1.0
C5 A:RTE501 4.1 32.2 0.5
CB A:GLU259 4.1 40.3 1.0
CD1 A:LEU255 4.3 30.8 1.0
F9 A:RTE501 4.3 32.2 0.5
CA A:GLU259 4.4 38.6 1.0
CZ A:ARG280 4.5 38.3 1.0
O7 A:RTE501 4.8 29.5 0.5
O7 A:RTE501 4.8 28.4 0.5
CG A:LEU255 4.8 28.9 1.0
OE1 A:GLU259 4.8 46.2 1.0
CD A:GLU259 4.8 45.4 1.0
O A:LEU255 4.9 27.5 1.0
NE A:ARG280 4.9 37.8 1.0
N A:GLU259 5.0 37.0 1.0

Fluorine binding site 2 out of 2 in 5z5s

Go back to Fluorine Binding Sites List in 5z5s
Fluorine binding site 2 out of 2 in the Crystal Structure of the Ppargamma-Lbd Complexed with Compound 13AB


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 the Ppargamma-Lbd Complexed with Compound 13AB within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:32.2
occ:0.50
F9 A:RTE501 0.0 32.2 0.5
C6 A:RTE501 1.1 33.4 0.5
C2 A:RTE501 1.3 31.8 0.5
C1 A:RTE501 1.9 33.2 0.5
C1 A:RTE501 2.3 31.5 0.5
C5 A:RTE501 2.3 32.2 0.5
C3 A:RTE501 2.3 30.8 0.5
CL1 A:RTE501 2.5 37.0 0.5
CD1 A:ILE341 2.9 29.2 1.0
CL1 A:RTE501 2.9 34.6 0.5
CD1 A:ILE249 3.0 27.2 1.0
C2 A:RTE501 3.2 33.1 0.5
CD1 A:ILE262 3.2 32.5 1.0
C4 A:RTE501 3.5 31.1 0.5
C6 A:RTE501 3.6 30.8 0.5
C4 A:RTE501 3.6 29.7 0.5
C3 A:RTE501 3.9 32.0 0.5
C5 A:RTE501 4.1 30.3 0.5
CG1 A:ILE341 4.2 27.9 1.0
F9 A:RTE501 4.3 33.4 0.5
CE A:MET348 4.3 30.9 1.0
CG1 A:ILE249 4.4 26.4 1.0
CG1 A:ILE262 4.4 33.8 1.0
CB A:ILE262 4.7 33.6 1.0
O7 A:RTE501 4.7 29.5 0.5
CD1 A:LEU255 4.8 30.8 1.0
O7 A:RTE501 4.8 28.4 0.5
CG2 A:ILE262 4.9 33.3 1.0
C8 A:RTE501 4.9 27.2 0.5
C8 A:RTE501 5.0 26.3 0.5

Reference:

T.Shinozuka, T.Tsukada, K.Fujii, E.Tokumaru, K.Shimada, Y.Onishi, Y.Matsui, S.Wakimoto, M.Kuroha, T.Ogata, K.Araki, J.Ohsumi, R.Sawamura, N.Watanabe, H.Yamamoto, K.Fujimoto, Y.Tani, M.Mori, J.Tanaka. Discovery of Ds-6930, A Potent Selective Ppar Gamma Modulator. Part I: Lead Identification. Bioorg. Med. Chem. V. 26 5079 2018.
ISSN: ESSN 1464-3391
PubMed: 30241907
DOI: 10.1016/J.BMC.2018.09.006
Page generated: Sun Dec 13 12:43:39 2020

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