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Fluorine in PDB 6xp9: Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1

Enzymatic activity of Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1

All present enzymatic activity of Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1:
2.3.1.48;

Protein crystallography data

The structure of Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1, PDB code: 6xp9 was solved by J.A.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.94 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.029, 88.613, 105.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1 (pdb code 6xp9). 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 Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1, PDB code: 6xp9:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6xp9

Go back to Fluorine Binding Sites List in 6xp9
Fluorine binding site 1 out of 2 in the Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:62.4
occ:1.00
F1 A:QCG501 0.0 62.4 1.0
C10 A:QCG501 1.4 62.1 1.0
C11 A:QCG501 2.3 61.1 1.0
C9 A:QCG501 2.4 62.9 1.0
H5 A:QCG501 2.6 69.4 0.0
O4 A:QCG501 2.7 60.7 1.0
C5 A:QCG501 3.6 64.1 1.0
C12 A:QCG501 3.6 61.4 1.0
CG A:MET246 3.9 41.7 1.0
OG A:SER247 3.9 48.9 1.0
O A:MET243 4.0 46.7 1.0
C28 A:QCG501 4.1 60.5 1.0
CB A:MET246 4.1 41.0 1.0
C13 A:QCG501 4.1 62.3 1.0
CA A:MET243 4.2 47.7 1.0
CB A:MET243 4.2 50.5 1.0
CG A:MET243 4.4 56.5 1.0
H27 A:QCG501 4.4 64.0 0.0
H28 A:QCG501 4.5 62.1 0.0
O3 A:QCG501 4.5 72.4 1.0
CE2 A:PHE288 4.6 40.4 1.0
C A:MET243 4.6 46.7 1.0
N A:SER247 4.6 40.5 1.0
CZ A:PHE288 4.7 39.9 1.0
C4 A:QCG501 4.8 66.7 1.0
C26 A:QCG501 4.9 60.6 1.0
C29 A:QCG501 4.9 60.4 1.0

Fluorine binding site 2 out of 2 in 6xp9

Go back to Fluorine Binding Sites List in 6xp9
Fluorine binding site 2 out of 2 in the Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Pregnane X Receptor Ligand Binding Domain Bound Tethered with Src Co-Activator Peptide in Complex with (S,S)-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:63.5
occ:1.00
F1 B:QCG502 0.0 63.5 1.0
C10 B:QCG502 1.4 63.9 1.0
C11 B:QCG502 2.4 62.9 1.0
C9 B:QCG502 2.4 64.9 1.0
H5 B:QCG502 2.6 75.0 0.0
O4 B:QCG502 2.7 61.9 1.0
C5 B:QCG502 3.6 66.0 1.0
C12 B:QCG502 3.6 63.1 1.0
O B:HOH621 3.6 68.4 1.0
CG B:MET246 3.8 43.8 1.0
O B:MET243 3.9 46.6 1.0
OG B:SER247 3.9 48.0 1.0
CB B:MET246 4.0 43.8 1.0
C28 B:QCG502 4.1 61.9 1.0
CA B:MET243 4.1 48.1 1.0
C13 B:QCG502 4.1 64.4 1.0
CB B:MET243 4.2 49.2 1.0
CG B:MET243 4.4 55.0 1.0
H27 B:QCG502 4.5 68.0 0.0
H28 B:QCG502 4.5 66.4 0.0
C B:MET243 4.5 47.4 1.0
N B:SER247 4.6 43.7 1.0
CE2 B:PHE288 4.6 41.2 1.0
CZ B:PHE288 4.7 40.9 1.0
O3 B:QCG502 4.7 73.1 1.0
C4 B:QCG502 4.8 68.4 1.0
C26 B:QCG502 4.9 62.4 1.0
C29 B:QCG502 4.9 62.1 1.0
H29 B:QCG502 4.9 65.7 0.0
C B:MET246 5.0 44.1 1.0

Reference:

P.Sivaprakasam, Z.Wang, N.A.Meanwell, J.A.Khan, D.R.Langley, S.R.Johnson, G.Li, A.Pendri, T.P.Connolly, M.Gao, D.M.Camac, C.Klakouski, T.Zvyaga, C.Cianci, B.Mcauliffe, B.Ding, L.Discotto, M.R.Krystal, S.Jenkins, K.M.Peese, B.Narasimhulu Naidu. Structure-Based Amelioration of Pxr Transactivation in A Novel Series of Macrocyclic Allosteric Inhibitors of Hiv-1 Integrase. Bioorg.Med.Chem.Lett. V. 30 27531 2020.
ISSN: ESSN 1464-3405
PubMed: 32890685
DOI: 10.1016/J.BMCL.2020.127531
Page generated: Fri Aug 2 04:16:12 2024

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