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Fluorine in PDB 4nz2: Crystal Structure of CYP2C9 in Complex with An Inhibitor

Enzymatic activity of Crystal Structure of CYP2C9 in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of CYP2C9 in Complex with An Inhibitor:
1.14.13.48; 1.14.13.49; 1.14.13.80;

Protein crystallography data

The structure of Crystal Structure of CYP2C9 in Complex with An Inhibitor, PDB code: 4nz2 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) 48.47 / 2.45
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.380, 164.380, 111.590, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 23.5

Other elements in 4nz2:

The structure of Crystal Structure of CYP2C9 in Complex with An Inhibitor also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of CYP2C9 in Complex with An Inhibitor (pdb code 4nz2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of CYP2C9 in Complex with An Inhibitor, PDB code: 4nz2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 1 out of 6 in the Crystal Structure of CYP2C9 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 CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:80.1
occ:1.00
 F24 A:2QJ504 0.0 80.1 1.0
C23 A:2QJ504 1.4 79.9 1.0
F25 A:2QJ504 2.2 79.9 1.0
F26 A:2QJ504 2.2 79.6 1.0
C2 A:2QJ504 2.4 80.0 1.0
O27 A:2QJ504 2.8 80.0 1.0
OD1 A:ASN107 2.9 83.7 1.0
C1 A:2QJ504 2.9 79.8 1.0
O A:ALA106 3.6 70.1 1.0
C3 A:2QJ504 3.7 79.8 1.0
CG2 A:VAL237 3.8 47.2 1.0
CG A:ASN107 3.9 89.7 1.0
CB A:ALA106 4.2 67.3 1.0
C A:ALA106 4.2 70.7 1.0
N5 A:2QJ504 4.4 79.4 1.0
O4 A:2QJ504 4.4 79.8 1.0
ND2 A:ASN107 4.6 81.5 1.0
N A:ASN107 4.8 67.1 1.0
CD2 A:LEU233 4.8 50.0 1.0
CA A:ALA106 4.9 67.2 1.0
CB A:LEU233 4.9 43.9 1.0
CA A:ASN107 5.0 66.7 1.0

Fluorine binding site 2 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 2 out of 6 in the Crystal Structure of CYP2C9 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 CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:79.9
occ:1.00
 F25 A:2QJ504 0.0 79.9 1.0
C23 A:2QJ504 1.4 79.9 1.0
F24 A:2QJ504 2.2 80.1 1.0
F26 A:2QJ504 2.2 79.6 1.0
C2 A:2QJ504 2.4 80.0 1.0
O27 A:2QJ504 2.7 80.0 1.0
C3 A:2QJ504 2.8 79.8 1.0
N5 A:2QJ504 3.0 79.4 1.0
O4 A:2QJ504 3.7 79.8 1.0
C1 A:2QJ504 3.7 79.8 1.0
CD1 A:LEU208 3.8 50.0 1.0
OD1 A:ASN107 4.0 83.7 1.0
C6 A:2QJ504 4.2 79.1 1.0
CD2 A:LEU208 4.3 53.0 1.0
CL1 A:2QJ504 4.4 79.3 1.0
CD2 A:LEU233 4.4 50.0 1.0
CG A:LEU208 4.5 50.4 1.0
CB A:ALA106 4.7 67.3 1.0
C11 A:2QJ504 4.7 79.2 1.0
CG A:ASN107 4.9 89.7 1.0
ND2 A:ASN107 4.9 81.5 1.0

Fluorine binding site 3 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 3 out of 6 in the Crystal Structure of CYP2C9 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 CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:79.6
occ:1.00
 F26 A:2QJ504 0.0 79.6 1.0
C23 A:2QJ504 1.4 79.9 1.0
F25 A:2QJ504 2.2 79.9 1.0
F24 A:2QJ504 2.2 80.1 1.0
C2 A:2QJ504 2.4 80.0 1.0
C3 A:2QJ504 2.8 79.8 1.0
C1 A:2QJ504 3.0 79.8 1.0
O4 A:2QJ504 3.0 79.8 1.0
CD2 A:LEU233 3.6 50.0 1.0
O27 A:2QJ504 3.6 80.0 1.0
ND2 A:ASN204 3.7 48.1 1.0
N5 A:2QJ504 3.8 79.4 1.0
CG2 A:VAL237 3.9 47.2 1.0
CG A:ASN204 4.0 57.9 1.0
O A:HOH681 4.1 56.7 1.0
CB A:ASN204 4.2 41.2 1.0
CD1 A:LEU208 4.4 50.0 1.0
OD1 A:ASN204 4.6 51.7 1.0
CG A:LEU233 4.6 48.1 1.0
CB A:LEU233 4.6 43.9 1.0
O A:LEU233 4.9 47.3 1.0
OD1 A:ASN107 5.0 83.7 1.0
C6 A:2QJ504 5.0 79.1 1.0

Fluorine binding site 4 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 4 out of 6 in the Crystal Structure of CYP2C9 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 4 of Crystal Structure of CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F504

b:77.1
occ:1.00
 F24 B:2QJ504 0.0 77.1 1.0
C23 B:2QJ504 1.4 77.4 1.0
F25 B:2QJ504 2.2 77.6 1.0
F26 B:2QJ504 2.2 77.3 1.0
C2 B:2QJ504 2.4 77.8 1.0
O27 B:2QJ504 2.8 77.7 1.0
C1 B:2QJ504 2.9 77.7 1.0
OD1 B:ASN107 3.3 85.7 1.0
CG2 B:VAL237 3.6 41.8 1.0
C3 B:2QJ504 3.7 78.1 1.0
CG B:ASN107 3.7 91.2 1.0
ND2 B:ASN107 3.7 83.8 1.0
O B:ALA106 3.8 68.2 1.0
C B:ALA106 4.3 68.9 1.0
O4 B:2QJ504 4.4 78.2 1.0
N5 B:2QJ504 4.4 78.1 1.0
CB B:ALA106 4.4 65.9 1.0
CD2 B:LEU233 4.8 45.8 1.0
N B:ASN107 4.8 64.9 1.0
CB B:ASN107 4.9 65.7 1.0
CA B:ASN107 4.9 64.5 1.0
CB B:VAL237 4.9 42.8 1.0

Fluorine binding site 5 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 5 out of 6 in the Crystal Structure of CYP2C9 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 5 of Crystal Structure of CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F504

b:77.6
occ:1.00
 F25 B:2QJ504 0.0 77.6 1.0
C23 B:2QJ504 1.4 77.4 1.0
F24 B:2QJ504 2.2 77.1 1.0
F26 B:2QJ504 2.2 77.3 1.0
C2 B:2QJ504 2.4 77.8 1.0
O27 B:2QJ504 2.8 77.7 1.0
C3 B:2QJ504 2.8 78.1 1.0
N5 B:2QJ504 3.1 78.1 1.0
O4 B:2QJ504 3.6 78.2 1.0
C1 B:2QJ504 3.7 77.7 1.0
CD1 B:LEU208 3.8 51.5 1.0
CD2 B:LEU233 4.1 45.8 1.0
OD1 B:ASN107 4.2 85.7 1.0
C6 B:2QJ504 4.3 78.5 1.0
CD2 B:LEU208 4.4 54.2 1.0
CG B:LEU208 4.5 51.6 1.0
CL1 B:2QJ504 4.6 79.3 1.0
CB B:ALA106 4.8 65.9 1.0
C11 B:2QJ504 4.9 79.0 1.0
CG B:LEU233 5.0 44.4 1.0

Fluorine binding site 6 out of 6 in 4nz2

Go back to Fluorine Binding Sites List in 4nz2
Fluorine binding site 6 out of 6 in the Crystal Structure of CYP2C9 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 6 of Crystal Structure of CYP2C9 in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F504

b:77.3
occ:1.00
 F26 B:2QJ504 0.0 77.3 1.0
C23 B:2QJ504 1.4 77.4 1.0
F25 B:2QJ504 2.2 77.6 1.0
F24 B:2QJ504 2.2 77.1 1.0
C2 B:2QJ504 2.4 77.8 1.0
C3 B:2QJ504 2.9 78.1 1.0
C1 B:2QJ504 3.0 77.7 1.0
O4 B:2QJ504 3.0 78.2 1.0
O27 B:2QJ504 3.6 77.7 1.0
CG2 B:VAL237 3.6 41.8 1.0
CD2 B:LEU233 3.8 45.8 1.0
ND2 B:ASN204 3.8 54.3 1.0
N5 B:2QJ504 3.9 78.1 1.0
CG B:ASN204 4.0 61.9 1.0
O B:HOH758 4.0 59.7 1.0
CB B:ASN204 4.3 40.9 1.0
OD1 B:ASN204 4.6 56.5 1.0
CD1 B:LEU208 4.8 51.5 1.0
CB B:LEU233 4.9 40.2 1.0
O B:LEU233 4.9 43.9 1.0
CG B:LEU233 4.9 44.4 1.0

Reference:

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
Page generated: Thu Aug 1 04:25:45 2024

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