Fluorine in PDB 5a5i: Cytochrome 2C9 P450 Inhibitor Complex

The structure of Cytochrome 2C9 P450 Inhibitor Complex, PDB code: 5a5i was solved by S.E.Skerratt, M.J.De Groot, C.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.63 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	92.217, 92.217, 170.414, 90.00, 90.00, 120.00
R / Rfree (%)	21.24 / 24.501

The structure of Cytochrome 2C9 P450 Inhibitor Complex also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Cytochrome 2C9 P450 Inhibitor Complex (pdb code 5a5i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cytochrome 2C9 P450 Inhibitor Complex, PDB code: 5a5i:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cytochrome 2C9 P450 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cytochrome 2C9 P450 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1493 b:52.8 occ:1.00 F1 A:XI11493 0.0 52.8 1.0 C2 A:XI11493 1.3 53.2 1.0 F3 A:XI11493 2.1 62.5 1.0 F4 A:XI11493 2.1 61.7 1.0 S5 A:XI11493 2.6 53.7 1.0 O7 A:XI11493 2.8 56.4 1.0 N8 A:XI11493 3.3 57.0 1.0 NE A:ARG108 3.4 61.7 1.0 CG A:ARG108 3.6 57.7 1.0 O6 A:XI11493 3.7 51.0 1.0 CB A:ARG108 4.0 54.3 1.0 CE2 A:PHE114 4.0 35.5 1.0 CD A:ARG108 4.1 57.0 1.0 CZ A:ARG108 4.2 61.9 1.0 NH2 A:ARG108 4.2 60.5 1.0 CD2 A:PHE114 4.6 32.4 1.0 C9 A:XI11493 4.7 63.0 1.0 CZ A:PHE114 4.7 31.1 1.0 CG2 A:VAL237 4.9 54.0 1.0 CD1 A:LEU208 5.0 63.1 1.0

Fluorine binding site 2 out of 3 in the Cytochrome 2C9 P450 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cytochrome 2C9 P450 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1493 b:62.5 occ:1.00 F3 A:XI11493 0.0 62.5 1.0 C2 A:XI11493 1.3 53.2 1.0 F4 A:XI11493 2.1 61.7 1.0 F1 A:XI11493 2.1 52.8 1.0 S5 A:XI11493 2.6 53.7 1.0 CD1 A:LEU208 3.0 63.1 1.0 N8 A:XI11493 3.0 57.0 1.0 O6 A:XI11493 3.1 51.0 1.0 C15 A:XI11493 3.6 69.7 1.0 O7 A:XI11493 3.7 56.4 1.0 C16 A:XI11493 3.8 67.8 1.0 C9 A:XI11493 4.0 63.0 1.0 CG A:LEU208 4.3 58.9 1.0 CD2 A:LEU208 4.4 57.8 1.0 CE2 A:PHE114 4.8 35.5 1.0 C13 A:XI11493 4.8 67.0 1.0

Fluorine binding site 3 out of 3 in the Cytochrome 2C9 P450 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cytochrome 2C9 P450 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1493 b:61.7 occ:1.00 F4 A:XI11493 0.0 61.7 1.0 C2 A:XI11493 1.3 53.2 1.0 F3 A:XI11493 2.1 62.5 1.0 F1 A:XI11493 2.1 52.8 1.0 S5 A:XI11493 2.6 53.7 1.0 O6 A:XI11493 2.9 51.0 1.0 O7 A:XI11493 3.1 56.4 1.0 CG2 A:VAL237 3.4 54.0 1.0 N8 A:XI11493 3.9 57.0 1.0 CG A:LEU233 4.0 60.8 1.0 CD2 A:LEU233 4.1 61.6 1.0 CD1 A:LEU208 4.2 63.1 1.0 ND2 A:ASN204 4.2 46.8 1.0 CD1 A:LEU233 4.4 59.0 1.0 NE A:ARG108 4.7 61.7 1.0 CG A:ARG108 4.7 57.7 1.0 CB A:VAL237 4.8 47.5 1.0 CG1 A:VAL237 5.0 50.5 1.0

S.E.Skerratt, M.J.De Groot, C.Phillips. Discovery of A Novel Binding Pocket For Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar. Med.Chem.Comm. V. 7 813 2016.
ISSN: ISSN 2040-2503
DOI: 10.1039/C6MD00011H