Fluorine in PDB 5wbg: Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz

The structure of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz, PDB code: 5wbg was solved by M.B.Shah, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.293, 197.786, 119.222, 90.00, 98.51, 90.00
R / Rfree (%)	22.7 / 26.2

The structure of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Chlorine	(Cl)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz (pdb code 5wbg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz, PDB code: 5wbg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:0.4 occ:1.00 FAC A:9ZJ502 0.0 0.4 1.0 CAT A:9ZJ502 1.3 0.4 1.0 FAD A:9ZJ502 2.2 0.7 1.0 FAB A:9ZJ502 2.2 0.8 1.0 CAJ A:9ZJ502 2.3 0.4 1.0 CAU A:9ZJ502 2.3 0.6 1.0 CAQ A:9ZJ502 2.5 1.0 1.0 CD1 A:ILE101 3.3 39.7 1.0 OAN A:9ZJ502 3.4 98.7 1.0 CAO A:9ZJ502 3.5 0.2 1.0 CZ A:PHE115 3.5 47.4 1.0 CAG A:9ZJ502 3.5 0.6 1.0 CAP A:9ZJ502 3.7 0.0 1.0 CE1 A:PHE115 4.2 46.2 1.0 CL A:9ZJ502 4.3 0.3 1.0 CAR A:9ZJ502 4.4 93.8 1.0 CE2 A:PHE115 4.4 48.4 1.0 CAH A:9ZJ502 4.4 0.3 1.0 NAM A:9ZJ502 4.5 0.6 1.0 CAI A:9ZJ502 4.5 0.7 1.0 CAF A:9ZJ502 4.6 95.2 1.0 CG1 A:ILE101 4.7 41.0 1.0 CG1 A:VAL367 4.8 23.9 1.0 CG2 A:ILE114 4.9 16.8 1.0 CG2 A:VAL104 5.0 32.7 1.0 CB A:ILE101 5.0 40.3 1.0

Fluorine binding site 2 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:0.7 occ:1.00 FAD A:9ZJ502 0.0 0.7 1.0 CAT A:9ZJ502 1.3 0.4 1.0 FAC A:9ZJ502 2.2 0.4 1.0 FAB A:9ZJ502 2.2 0.8 1.0 CAU A:9ZJ502 2.3 0.6 1.0 OAN A:9ZJ502 2.7 98.7 1.0 CAG A:9ZJ502 3.1 0.6 1.0 CD1 A:ILE101 3.2 39.7 1.0 CAQ A:9ZJ502 3.5 1.0 1.0 CG1 A:VAL477 3.6 33.2 1.0 CG2 A:VAL367 3.8 26.2 1.0 CAJ A:9ZJ502 3.9 0.4 1.0 CAR A:9ZJ502 4.0 93.8 1.0 CG1 A:VAL367 4.0 23.9 1.0 CAF A:9ZJ502 4.1 95.2 1.0 CB A:VAL367 4.4 31.4 1.0 CAP A:9ZJ502 4.5 0.0 1.0 CG1 A:ILE101 4.6 41.0 1.0 NAM A:9ZJ502 4.8 0.6 1.0 CD2 A:LEU363 4.9 20.9 1.0 CB A:VAL477 4.9 43.2 1.0 CAA A:9ZJ502 4.9 89.4 1.0

Fluorine binding site 3 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:0.8 occ:1.00 FAB A:9ZJ502 0.0 0.8 1.0 CAT A:9ZJ502 1.3 0.4 1.0 FAC A:9ZJ502 2.2 0.4 1.0 FAD A:9ZJ502 2.2 0.7 1.0 CAU A:9ZJ502 2.3 0.6 1.0 CAG A:9ZJ502 2.5 0.6 1.0 CAJ A:9ZJ502 3.0 0.4 1.0 CAQ A:9ZJ502 3.1 1.0 1.0 CAF A:9ZJ502 3.3 95.2 1.0 OAN A:9ZJ502 3.4 98.7 1.0 CG1 A:VAL477 4.1 33.2 1.0 CD1 A:ILE101 4.2 39.7 1.0 CAO A:9ZJ502 4.3 0.2 1.0 CAS A:9ZJ502 4.4 93.4 1.0 CAP A:9ZJ502 4.4 0.0 1.0 CG2 A:ILE209 4.5 35.7 1.0 CAR A:9ZJ502 4.7 93.8 1.0 CD1 A:ILE209 4.7 16.9 1.0 CB A:VAL477 4.8 43.2 1.0 CAK A:9ZJ502 4.8 92.2 1.0

Fluorine binding site 4 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:0.1 occ:1.00 FAC B:9ZJ502 0.0 0.1 1.0 CAT B:9ZJ502 1.3 0.1 1.0 FAB B:9ZJ502 2.2 95.8 1.0 FAD B:9ZJ502 2.2 0.0 1.0 CAJ B:9ZJ502 2.3 99.1 1.0 CAU B:9ZJ502 2.3 0.3 1.0 CAQ B:9ZJ502 2.5 0.2 1.0 CD1 B:ILE101 3.4 40.8 1.0 OAN B:9ZJ502 3.4 96.4 1.0 CAO B:9ZJ502 3.5 0.8 1.0 CAG B:9ZJ502 3.5 0.1 1.0 CZ B:PHE115 3.6 44.5 1.0 CAP B:9ZJ502 3.7 0.6 1.0 CE1 B:PHE115 4.2 36.8 1.0 CL B:9ZJ502 4.3 94.2 1.0 CAR B:9ZJ502 4.4 0.9 1.0 CAH B:9ZJ502 4.4 0.2 1.0 CE2 B:PHE115 4.4 32.4 1.0 NAM B:9ZJ502 4.5 0.6 1.0 CAI B:9ZJ502 4.5 0.3 1.0 CAF B:9ZJ502 4.6 0.2 1.0 CG1 B:ILE101 4.7 38.9 1.0 CG1 B:VAL367 4.8 27.7 1.0 CG2 B:VAL104 5.0 32.3 1.0 CB B:ILE101 5.0 37.4 1.0

Fluorine binding site 5 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:0.0 occ:1.00 FAD B:9ZJ502 0.0 0.0 1.0 CAT B:9ZJ502 1.3 0.1 1.0 FAB B:9ZJ502 2.2 95.8 1.0 FAC B:9ZJ502 2.2 0.1 1.0 CAU B:9ZJ502 2.3 0.3 1.0 OAN B:9ZJ502 2.6 96.4 1.0 CAG B:9ZJ502 3.1 0.1 1.0 CD1 B:ILE101 3.2 40.8 1.0 CAQ B:9ZJ502 3.5 0.2 1.0 CG1 B:VAL477 3.6 39.1 1.0 CG2 B:VAL367 3.7 30.2 1.0 CAJ B:9ZJ502 3.9 99.1 1.0 CAR B:9ZJ502 4.0 0.9 1.0 CG1 B:VAL367 4.0 27.7 1.0 CAF B:9ZJ502 4.1 0.2 1.0 CB B:VAL367 4.4 33.5 1.0 CAP B:9ZJ502 4.5 0.6 1.0 CG1 B:ILE101 4.7 38.9 1.0 NAM B:9ZJ502 4.8 0.6 1.0 CAA B:9ZJ502 4.8 0.4 1.0 CB B:VAL477 4.9 46.0 1.0

Fluorine binding site 6 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


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 Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:95.8 occ:1.00 FAB B:9ZJ502 0.0 95.8 1.0 CAT B:9ZJ502 1.3 0.1 1.0 FAD B:9ZJ502 2.2 0.0 1.0 FAC B:9ZJ502 2.2 0.1 1.0 CAU B:9ZJ502 2.3 0.3 1.0 CAG B:9ZJ502 2.5 0.1 1.0 CAJ B:9ZJ502 3.0 99.1 1.0 CAQ B:9ZJ502 3.1 0.2 1.0 CAF B:9ZJ502 3.3 0.2 1.0 OAN B:9ZJ502 3.3 96.4 1.0 CG1 B:VAL477 4.0 39.1 1.0 CD1 B:ILE101 4.3 40.8 1.0 CAO B:9ZJ502 4.3 0.8 1.0 CAS B:9ZJ502 4.4 0.9 1.0 CAP B:9ZJ502 4.4 0.6 1.0 CG2 B:ILE209 4.6 24.8 1.0 CAR B:9ZJ502 4.8 0.9 1.0 CB B:VAL477 4.8 46.0 1.0 CAK B:9ZJ502 4.8 0.3 1.0 CD1 B:ILE209 4.8 19.1 1.0

Fluorine binding site 7 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:84.8 occ:1.00 FAC C:9ZJ502 0.0 84.8 1.0 CAT C:9ZJ502 1.3 86.8 1.0 FAB C:9ZJ502 2.2 85.8 1.0 FAD C:9ZJ502 2.2 86.3 1.0 CAJ C:9ZJ502 2.3 91.5 1.0 CAU C:9ZJ502 2.3 86.9 1.0 CAQ C:9ZJ502 2.5 88.9 1.0 CD1 C:ILE101 3.0 49.2 1.0 OAN C:9ZJ502 3.3 81.4 1.0 CAO C:9ZJ502 3.5 94.3 1.0 CZ C:PHE115 3.5 45.4 1.0 CAG C:9ZJ502 3.5 87.8 1.0 CAP C:9ZJ502 3.7 92.4 1.0 CE1 C:PHE115 4.2 43.1 1.0 CL C:9ZJ502 4.3 88.7 1.0 CAR C:9ZJ502 4.3 81.0 1.0 CG1 C:ILE101 4.4 41.7 1.0 CAH C:9ZJ502 4.4 98.2 1.0 CE2 C:PHE115 4.4 45.1 1.0 NAM C:9ZJ502 4.5 87.0 1.0 CAI C:9ZJ502 4.5 99.7 1.0 CAF C:9ZJ502 4.6 90.0 1.0 CG1 C:VAL367 4.8 38.2 1.0 CG2 C:VAL104 5.0 23.6 1.0 CB C:ILE101 5.0 42.5 1.0

Fluorine binding site 8 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:86.3 occ:1.00 FAD C:9ZJ502 0.0 86.3 1.0 CAT C:9ZJ502 1.3 86.8 1.0 FAB C:9ZJ502 2.2 85.8 1.0 FAC C:9ZJ502 2.2 84.8 1.0 CAU C:9ZJ502 2.3 86.9 1.0 OAN C:9ZJ502 2.6 81.4 1.0 CAG C:9ZJ502 3.1 87.8 1.0 CD1 C:ILE101 3.1 49.2 1.0 CAQ C:9ZJ502 3.5 88.9 1.0 CG1 C:VAL477 3.6 34.3 1.0 CG2 C:VAL367 3.7 38.9 1.0 CAR C:9ZJ502 3.9 81.0 1.0 CAJ C:9ZJ502 3.9 91.5 1.0 CG1 C:VAL367 4.0 38.2 1.0 CAF C:9ZJ502 4.1 90.0 1.0 CB C:VAL367 4.4 39.8 1.0 CG1 C:ILE101 4.5 41.7 1.0 CAP C:9ZJ502 4.5 92.4 1.0 NAM C:9ZJ502 4.8 87.0 1.0 CB C:VAL477 4.8 43.1 1.0 CAA C:9ZJ502 4.9 73.3 1.0

Fluorine binding site 9 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:85.8 occ:1.00 FAB C:9ZJ502 0.0 85.8 1.0 CAT C:9ZJ502 1.3 86.8 1.0 FAC C:9ZJ502 2.2 84.8 1.0 FAD C:9ZJ502 2.2 86.3 1.0 CAU C:9ZJ502 2.3 86.9 1.0 CAG C:9ZJ502 2.5 87.8 1.0 CAJ C:9ZJ502 3.0 91.5 1.0 CAQ C:9ZJ502 3.1 88.9 1.0 CAF C:9ZJ502 3.3 90.0 1.0 OAN C:9ZJ502 3.4 81.4 1.0 CD1 C:ILE101 3.9 49.2 1.0 CG1 C:VAL477 4.0 34.3 1.0 CAO C:9ZJ502 4.3 94.3 1.0 CAS C:9ZJ502 4.4 92.3 1.0 CAP C:9ZJ502 4.4 92.4 1.0 CG2 C:ILE209 4.5 31.1 1.0 CAR C:9ZJ502 4.7 81.0 1.0 CB C:VAL477 4.8 43.1 1.0 CAK C:9ZJ502 4.8 91.6 1.0 CD1 C:ILE209 4.8 35.2 1.0

Fluorine binding site 10 out of 18 in the Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Cytochrome P450 2B6 (Y226H/K262R) in Complex with An Analog of A Drug Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ D:F502 b:79.3 occ:1.00 FAC D:9ZJ502 0.0 79.3 1.0 CAT D:9ZJ502 1.3 90.5 1.0 FAB D:9ZJ502 2.2 92.0 1.0 FAD D:9ZJ502 2.2 93.0 1.0 CAJ D:9ZJ502 2.3 0.3 1.0 CAU D:9ZJ502 2.3 94.7 1.0 CAQ D:9ZJ502 2.5 98.0 1.0 CD1 D:ILE101 3.2 26.1 1.0 CZ D:PHE115 3.4 48.4 1.0 OAN D:9ZJ502 3.5 92.7 1.0 CAO D:9ZJ502 3.5 0.5 1.0 CAG D:9ZJ502 3.5 98.9 1.0 CAP D:9ZJ502 3.7 0.3 1.0 CE1 D:PHE115 4.1 46.4 1.0 CL D:9ZJ502 4.3 0.5 1.0 CAR D:9ZJ502 4.4 90.2 1.0 CE2 D:PHE115 4.4 54.2 1.0 CAH D:9ZJ502 4.4 0.7 1.0 NAM D:9ZJ502 4.5 97.5 1.0 CAI D:9ZJ502 4.5 0.2 1.0 CG1 D:ILE101 4.6 26.4 1.0 CAF D:9ZJ502 4.6 0.8 1.0 CG1 D:VAL367 4.9 40.6 1.0 CG2 D:VAL104 4.9 43.2 1.0 CB D:ILE101 5.0 31.0 1.0 CG2 D:ILE114 5.0 47.7 1.0

M.B.Shah, Q.Zhang, J.R.Halpert. Crystal Structure of CYP2B6 in Complex with An Efavirenz Analog. Int J Mol Sci V. 19 2018.
ISSN: ESSN 1422-0067
PubMed: 29596329
DOI: 10.3390/IJMS19041025