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

Protein crystallography data

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

Other elements in 5a5i:

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

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

Fluorine Binding Sites:

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 5a5i

Go back to Fluorine Binding Sites List in 5a5i
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 5a5i

Go back to Fluorine Binding Sites List in 5a5i
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 5a5i

Go back to Fluorine Binding Sites List in 5a5i
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

Reference:

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
Page generated: Tue Jul 15 02:09:45 2025

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