Fluorine in PDB 5tbp: Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003

The structure of Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003, PDB code: 5tbp was solved by A.E.Aleshin, R.C.Liddington, Y.Su, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.15 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.640, 99.380, 109.860, 90.00, 99.15, 90.00
R / Rfree (%)	19.6 / 24.2

The binding sites of Fluorine atom in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 (pdb code 5tbp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003, PDB code: 5tbp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:64.0 occ:0.94 F21 A:7A4501 0.0 64.0 0.9 C19 A:7A4501 1.3 63.6 0.9 C20 A:7A4501 2.4 64.0 0.9 C18 A:7A4501 2.4 65.3 0.9 H11 A:7A4501 2.6 76.7 0.9 H20 A:7A4501 2.6 78.3 0.9 HD11 C:LEU451 2.7 80.9 1.0 HB3 A:LEU301 2.9 49.1 1.0 HA A:ARG302 2.9 64.2 1.0 HB2 A:LEU301 3.3 49.1 1.0 C A:LEU301 3.3 48.8 1.0 N A:ARG302 3.4 53.5 1.0 O A:LEU301 3.4 46.5 1.0 HG3 A:ARG302 3.4 83.6 1.0 CB A:LEU301 3.5 40.9 1.0 HD13 C:LEU451 3.5 80.9 1.0 CD1 C:LEU451 3.5 67.4 1.0 CA A:ARG302 3.6 53.5 1.0 C04 A:7A4501 3.6 68.3 0.9 C17 A:7A4501 3.7 61.3 0.9 HD21 C:LEU451 3.7 78.4 1.0 H A:ARG302 3.7 64.2 1.0 HD1 A:TRP305 3.7 62.6 1.0 CA A:LEU301 4.0 45.6 1.0 CG A:ARG302 4.1 69.7 1.0 HG2 A:ARG302 4.1 83.6 1.0 HD12 C:LEU451 4.1 80.9 1.0 C05 A:7A4501 4.2 65.9 0.9 HB3 A:TRP305 4.2 49.3 1.0 HG21 C:ILE447 4.2 0.1 1.0 CB A:ARG302 4.2 60.7 1.0 CD2 C:LEU451 4.4 65.3 1.0 HD22 C:LEU451 4.4 78.4 1.0 HB2 A:ARG302 4.4 72.9 1.0 CD1 A:TRP305 4.4 52.1 1.0 HD11 A:LEU276 4.4 69.4 1.0 H19 A:7A4501 4.4 73.5 0.9 HG22 C:ILE447 4.5 0.1 1.0 O A:VAL298 4.5 55.1 1.0 CG C:LEU451 4.5 68.5 1.0 HD13 A:LEU301 4.6 64.0 1.0 HG23 C:ILE447 4.6 0.1 1.0 HA A:LEU301 4.6 54.7 1.0 CG2 C:ILE447 4.6 90.1 1.0 HG13 A:VAL298 4.7 68.2 1.0 CG A:LEU301 4.8 46.6 1.0 HG C:LEU451 4.8 82.3 1.0 C A:ARG302 4.8 49.8 1.0 HD12 A:LEU301 4.9 64.0 1.0 CG A:TRP305 5.0 48.8 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:73.3 occ:0.87 F21 A:7A4502 0.0 73.3 0.9 C19 A:7A4502 1.3 74.6 0.9 C20 A:7A4502 2.4 77.7 0.9 C18 A:7A4502 2.4 77.6 0.9 HB1 A:ALA271 2.5 88.1 1.0 H11 A:7A4502 2.6 93.2 0.9 H20 A:7A4502 2.6 93.1 0.9 HG23 A:THR328 2.9 98.5 1.0 HB2 A:GLN275 3.0 77.7 1.0 O A:ALA271 3.2 73.3 1.0 HB3 A:ALA327 3.3 92.3 1.0 CB A:ALA271 3.3 73.4 1.0 HB3 A:ALA271 3.4 88.1 1.0 C A:ALA271 3.4 68.2 1.0 HG22 A:THR328 3.4 98.5 1.0 CG2 A:THR328 3.5 82.1 1.0 HA A:ALA272 3.6 79.5 1.0 C04 A:7A4502 3.6 77.8 0.9 C17 A:7A4502 3.7 78.3 0.9 HG21 A:THR328 3.7 98.5 1.0 N A:ALA272 3.9 67.2 1.0 CA A:ALA271 3.9 71.2 1.0 OE1 A:GLN275 3.9 65.7 1.0 CB A:GLN275 3.9 64.7 1.0 HB2 A:ALA271 4.1 88.1 1.0 HG2 A:GLN275 4.1 87.6 1.0 C05 A:7A4502 4.2 80.6 0.9 HA A:ALA271 4.2 85.5 1.0 CB A:ALA327 4.2 76.9 1.0 HB3 A:GLN275 4.2 77.7 1.0 CD A:GLN275 4.2 74.3 1.0 CA A:ALA272 4.3 66.2 1.0 CG A:GLN275 4.3 73.0 1.0 H A:ALA272 4.3 80.7 1.0 H A:GLN275 4.4 72.3 1.0 HB1 A:ALA327 4.4 92.3 1.0 H19 A:7A4502 4.5 94.0 0.9 H3 A:7A4501 4.5 93.4 0.9 H A:THR328 4.5 98.5 1.0 HB2 A:ALA327 4.7 92.3 1.0 N A:THR328 4.7 82.0 1.0 CB A:THR328 4.9 86.7 1.0 H A:ALA327 4.9 91.1 1.0 HB2 A:ALA272 5.0 81.5 1.0 N A:GLN275 5.0 60.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:97.4 occ:0.89 F21 A:7A4503 0.0 97.4 0.9 C19 A:7A4503 1.3 94.4 0.9 C20 A:7A4503 2.4 91.8 0.9 C18 A:7A4503 2.4 92.2 0.9 HD22 A:LEU436 2.5 94.3 1.0 H20 A:7A4503 2.6 0.7 0.9 H11 A:7A4503 2.6 0.2 0.9 HD13 A:LEU436 3.3 0.6 1.0 CD2 A:LEU436 3.4 78.6 1.0 C04 A:7A4503 3.6 90.1 0.9 C17 A:7A4503 3.7 90.2 0.9 HD21 A:LEU436 3.7 94.3 1.0 HB3 A:LEU436 3.7 94.5 1.0 HB2 A:PHE439 3.7 0.7 1.0 H32 C:GOL501 3.8 0.7 1.0 HB3 A:PHE439 3.8 0.7 1.0 HO3 C:GOL501 3.8 0.5 1.0 HD23 A:LEU436 4.0 94.3 1.0 CD1 A:LEU436 4.0 88.0 1.0 O3 C:GOL501 4.1 92.9 1.0 HD22 C:LEU433 4.1 0.4 1.0 CB A:PHE439 4.1 89.7 1.0 CG A:LEU436 4.1 82.0 1.0 CG A:PHE439 4.2 93.1 1.0 C05 A:7A4503 4.2 90.1 0.9 HD11 A:LEU436 4.3 0.6 1.0 C3 C:GOL501 4.4 93.9 1.0 CB A:LEU436 4.4 78.7 1.0 H19 A:7A4503 4.4 0.2 0.9 CD2 A:PHE439 4.5 93.1 1.0 HD2 A:PHE439 4.5 0.7 1.0 CD1 A:PHE439 4.6 93.7 1.0 HD1 A:PHE439 4.8 0.4 1.0 HD12 A:LEU436 4.9 0.6 1.0 H31 C:GOL501 4.9 0.7 1.0 HD23 C:LEU433 4.9 0.4 1.0 CD2 C:LEU433 4.9 85.3 1.0 HZ2 C:TRP305 5.0 96.1 1.0 HB2 A:LEU436 5.0 94.5 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:97.4 occ:0.87 F21 B:7A4501 0.0 97.4 0.9 C19 B:7A4501 1.3 93.6 0.9 C20 B:7A4501 2.4 90.8 0.9 C18 B:7A4501 2.4 91.8 0.9 H11 B:7A4501 2.6 0.9 0.9 H20 B:7A4501 2.6 0.1 0.9 HD13 D:LEU436 2.7 94.4 1.0 HD22 D:LEU436 2.8 94.5 1.0 CD1 D:LEU436 3.5 78.7 1.0 C04 B:7A4501 3.6 96.8 0.9 CD2 D:LEU436 3.6 78.7 1.0 C17 B:7A4501 3.7 89.1 0.9 HD11 D:LEU436 3.7 94.4 1.0 HB3 D:LEU436 3.8 92.1 1.0 HD22 B:LEU433 3.8 99.2 1.0 HD21 D:LEU436 3.8 94.5 1.0 HB2 D:PHE439 3.9 99.2 1.0 HB3 D:PHE439 4.0 99.2 1.0 CG D:LEU436 4.0 78.4 1.0 C05 B:7A4501 4.2 89.3 0.9 HD12 D:LEU436 4.2 94.4 1.0 CG D:PHE439 4.3 87.4 1.0 CB D:PHE439 4.3 82.7 1.0 HO3 B:GOL502 4.3 0.8 1.0 CB D:LEU436 4.4 76.8 1.0 HD23 D:LEU436 4.4 94.5 1.0 H19 B:7A4501 4.5 0.9 0.9 CD2 D:PHE439 4.5 85.4 1.0 HZ2 B:TRP305 4.6 85.4 1.0 HD2 D:PHE439 4.6 0.4 1.0 O3 B:GOL502 4.6 99.0 0.9 CD1 D:PHE439 4.6 85.5 1.0 CD2 B:LEU433 4.7 82.7 1.0 H32 B:GOL502 4.7 0.6 1.0 HD23 B:LEU433 4.7 99.2 1.0 HB2 D:LEU436 4.7 92.1 1.0 HD1 D:PHE439 4.8 0.6 1.0 HG D:LEU436 4.9 94.1 1.0 HB3 B:LEU433 4.9 85.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:79.2 occ:0.87 F21 D:7A4501 0.0 79.2 0.9 C19 D:7A4501 1.3 73.1 0.9 C20 D:7A4501 2.4 73.0 0.9 C18 D:7A4501 2.4 70.8 0.9 HD11 B:LEU451 2.6 97.3 1.0 H11 D:7A4501 2.6 87.7 0.9 H20 D:7A4501 2.6 84.9 0.9 HB3 D:LEU301 2.6 75.6 1.0 HB2 D:LEU301 3.0 75.6 1.0 HD13 B:LEU451 3.2 97.3 1.0 CB D:LEU301 3.2 63.0 1.0 C D:LEU301 3.2 65.0 1.0 HA D:ARG302 3.2 80.8 1.0 CD1 B:LEU451 3.3 81.1 1.0 O D:LEU301 3.3 61.4 1.0 N D:ARG302 3.4 63.5 1.0 HD21 B:LEU451 3.4 98.2 1.0 C04 D:7A4501 3.6 73.8 0.9 C17 D:7A4501 3.7 71.3 0.9 H D:ARG302 3.7 76.2 1.0 HG3 D:ARG302 3.7 97.0 1.0 CA D:ARG302 3.8 67.3 1.0 CA D:LEU301 3.8 63.3 1.0 HD22 B:LEU451 3.9 98.2 1.0 HD12 B:LEU451 3.9 97.3 1.0 HD1 D:TRP305 4.0 78.8 1.0 CD2 B:LEU451 4.0 81.8 1.0 C05 D:7A4501 4.2 74.5 0.9 O D:VAL298 4.2 68.7 1.0 CG B:LEU451 4.2 83.2 1.0 HD13 D:LEU301 4.3 83.4 1.0 HG2 D:ARG302 4.3 97.0 1.0 HG13 D:VAL298 4.3 95.1 1.0 CG D:ARG302 4.3 80.8 1.0 HG21 B:ILE447 4.4 0.1 1.0 HA D:LEU301 4.4 76.0 1.0 HB3 D:TRP305 4.4 64.2 1.0 H19 D:7A4501 4.4 85.6 0.9 CG D:LEU301 4.5 65.8 1.0 HD11 D:LEU276 4.5 75.2 1.0 CB D:ARG302 4.6 71.2 1.0 HG22 B:ILE447 4.6 0.1 1.0 CD1 D:TRP305 4.6 65.7 1.0 HD12 D:LEU301 4.6 83.4 1.0 HG B:LEU451 4.7 99.9 1.0 HA D:VAL298 4.7 82.4 1.0 CD1 D:LEU301 4.7 69.5 1.0 HB2 D:ARG302 4.8 85.5 1.0 HG23 B:ILE447 4.8 0.1 1.0 HD22 D:LEU301 4.8 78.4 1.0 CG2 B:ILE447 4.8 89.3 1.0 N D:LEU301 4.9 62.7 1.0 H D:LEU301 4.9 75.3 1.0 HD23 B:LEU451 4.9 98.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003


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 Rxr-Alpha Ligand Binding Domain Complexed with Synthetic Modulator K8003 within 5.0Å range: probe atom residue distance (Å) B Occ D:F502 b:80.0 occ:0.94 F21 D:7A4502 0.0 80.0 0.9 C19 D:7A4502 1.3 82.5 0.9 C20 D:7A4502 2.4 85.9 0.9 C18 D:7A4502 2.4 83.5 0.9 HB1 D:ALA271 2.4 78.2 1.0 H11 D:7A4502 2.6 0.0 0.9 H20 D:7A4502 2.6 0.2 0.9 O D:ALA271 2.7 69.3 1.0 HB2 D:GLN275 2.8 82.3 1.0 C D:ALA271 2.9 66.5 1.0 CB D:ALA271 3.1 65.1 1.0 HB3 D:ALA271 3.1 78.2 1.0 HA D:ALA272 3.1 74.8 1.0 HG23 D:THR328 3.4 0.4 1.0 N D:ALA272 3.4 65.1 1.0 HB3 D:ALA327 3.5 98.6 1.0 CA D:ALA271 3.5 65.7 1.0 C04 D:7A4502 3.6 83.6 0.9 CB D:GLN275 3.6 68.6 1.0 C17 D:7A4502 3.7 87.8 0.9 CA D:ALA272 3.7 62.3 1.0 HB3 D:GLN275 3.8 82.3 1.0 HG22 D:THR328 3.9 0.4 1.0 H D:ALA272 3.9 78.2 1.0 HA D:ALA271 3.9 78.8 1.0 HB2 D:ALA271 3.9 78.2 1.0 CG2 D:THR328 4.0 85.4 1.0 H D:GLN275 4.0 75.5 1.0 HG2 D:GLN275 4.0 94.5 1.0 H4 D:7A4501 4.1 89.3 0.9 HG21 D:THR328 4.1 0.4 1.0 C05 D:7A4502 4.2 87.6 0.9 CG D:GLN275 4.2 78.7 1.0 OE1 D:GLN275 4.3 80.7 1.0 CB D:ALA327 4.4 82.2 1.0 HB2 D:ALA272 4.4 78.4 1.0 H19 D:7A4502 4.5 0.3 0.9 CD D:GLN275 4.5 83.4 1.0 HB1 D:ALA327 4.5 98.6 1.0 N D:GLN275 4.7 62.9 1.0 CB D:ALA272 4.7 65.3 1.0 O D:ILE268 4.8 67.0 1.0 CA D:GLN275 4.8 65.4 1.0 HB2 D:ALA327 4.8 98.6 1.0 N D:ALA271 4.8 68.4 1.0 C D:ALA272 4.8 63.4 1.0 H3 D:7A4501 4.9 89.3 0.9 C16 D:7A4501 4.9 74.5 0.9 H D:THR328 5.0 0.8 1.0

L.Chen, A.E.Aleshin, G.Alitongbieke, Y.Zhou, X.Zhang, X.Ye, M.Hu, G.Ren, Z.Chen, Y.Ma, D.Zhang, S.Liu, W.Gao, L.Cai, L.Wu, Z.Zeng, F.Jiang, J.Liu, H.Zhou, G.Cadwell, R.C.Liddington, Y.Su, X.K.Zhang. Modulation of Nongenomic Activation of PI3K Signalling By Tetramerization of N-Terminally-Cleaved Rxr Alpha. Nat Commun V. 8 16066 2017.
ISSN: ESSN 2041-1723
PubMed: 28714476
DOI: 10.1038/NCOMMS16066