Fluorine in PDB 4ny4: Crystal Structure of CYP3A4 in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of CYP3A4 in Complex with An Inhibitor:
1.14.13.157; 1.14.13.32; 1.14.13.67; 1.14.13.97;

The structure of Crystal Structure of CYP3A4 in Complex with An Inhibitor, PDB code: 4ny4 was solved by G.Branden, T.Sjogren, Y.Xue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 2.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.548, 101.692, 132.422, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 27.3

The structure of Crystal Structure of CYP3A4 in Complex with An Inhibitor also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of CYP3A4 in Complex with An Inhibitor (pdb code 4ny4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of CYP3A4 in Complex with An Inhibitor, PDB code: 4ny4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of CYP3A4 in Complex with An Inhibitor


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 CYP3A4 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:0.6 occ:1.00 F20 A:2QH602 0.0 0.6 1.0 C14 A:2QH602 1.4 0.9 1.0 F21 A:2QH602 2.3 0.8 1.0 C13 A:2QH602 2.4 0.4 1.0 C15 A:2QH602 2.4 0.7 1.0 N16 A:2QH602 3.0 0.4 1.0 N12 A:2QH602 3.1 0.0 1.0 C11 A:2QH602 3.3 0.1 1.0 C17 A:2QH602 4.0 0.3 1.0 O A:ARG106 4.1 99.6 1.0 OE1 A:GLU374 4.2 0.1 1.0 CB A:ARG106 4.3 96.2 1.0 C23 A:2QH602 4.3 0.0 1.0 N19 A:2QH602 4.6 0.2 1.0 N A:ARG106 4.6 97.5 1.0 C10 A:2QH602 4.6 0.2 1.0 CA A:ARG106 4.8 97.3 1.0 N18 A:2QH602 4.8 0.3 1.0 C A:ARG106 4.9 0.3 1.0 CD A:ARG105 4.9 0.9 1.0 CD A:GLU374 5.0 0.3 1.0 C22 A:2QH602 5.0 0.6 1.0 CB A:ARG105 5.0 95.8 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of CYP3A4 in Complex with An Inhibitor


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 CYP3A4 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:0.8 occ:1.00 F21 A:2QH602 0.0 0.8 1.0 C14 A:2QH602 1.4 0.9 1.0 F20 A:2QH602 2.3 0.6 1.0 C13 A:2QH602 2.4 0.4 1.0 C15 A:2QH602 2.4 0.7 1.0 O A:ARG106 3.1 99.6 1.0 N16 A:2QH602 3.7 0.4 1.0 N12 A:2QH602 3.7 0.0 1.0 CB A:ARG106 3.8 96.2 1.0 CD A:ARG106 3.9 0.7 1.0 C A:ARG106 3.9 0.3 1.0 CB A:PHE108 3.9 98.3 1.0 CD1 A:PHE108 4.1 0.1 1.0 C11 A:2QH602 4.2 0.1 1.0 NE A:ARG106 4.3 0.6 1.0 CA A:ARG106 4.3 97.3 1.0 CG A:ARG106 4.3 0.8 1.0 CG A:PHE108 4.4 99.2 1.0 N A:PHE108 4.4 98.6 1.0 CA A:PHE108 4.6 97.8 1.0 CE1 A:PHE215 4.6 0.2 1.0 CZ A:PHE215 4.7 0.6 1.0 C A:PRO107 4.7 0.7 1.0 N A:ARG106 4.7 97.5 1.0 OE1 A:GLU374 4.8 0.1 1.0 C17 A:2QH602 4.9 0.3 1.0 N A:PRO107 4.9 99.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of CYP3A4 in Complex with An Inhibitor


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 CYP3A4 in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:0.1 occ:1.00 F34 A:2QH602 0.0 0.1 1.0 C25 A:2QH602 1.4 0.2 1.0 C24 A:2QH602 2.4 0.2 1.0 C26 A:2QH602 2.4 1.0 1.0 C28 A:2QH602 2.8 0.1 1.0 CB A:ALA370 3.1 77.5 1.0 C29 A:2QH602 3.2 0.2 1.0 CA A:ALA370 3.5 76.8 1.0 C23 A:2QH602 3.6 0.0 1.0 C27 A:2QH602 3.6 0.3 1.0 C33 A:2QH602 3.7 0.1 1.0 C3A A:HEM601 4.1 84.8 1.0 C22 A:2QH602 4.1 0.6 1.0 C30 A:2QH602 4.3 0.5 1.0 C2A A:HEM601 4.3 85.4 1.0 CMA A:HEM601 4.3 86.3 1.0 N A:ALA370 4.4 77.1 1.0 C4A A:HEM601 4.4 83.9 1.0 N32 A:2QH602 4.6 0.9 1.0 C A:ALA370 4.6 81.5 1.0 CAA A:HEM601 4.7 87.6 1.0 O A:ALA370 4.7 81.6 1.0 C1A A:HEM601 4.7 84.9 1.0 CD1 A:ILE369 4.8 90.4 1.0 CHB A:HEM601 4.8 83.9 1.0 NA A:HEM601 4.8 84.2 1.0 C31 A:2QH602 4.9 0.8 1.0

G.Branden, T.Sjogren, V.Schnecke, Y.Xue. Structure-Based Ligand Design to Overcome Cyp Inhibition in Drug Discovery Projects. Drug Discov Today V. 19 905 2014.
ISSN: ISSN 1359-6446
PubMed: 24642031
DOI: 10.1016/J.DRUDIS.2014.03.012