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Iron in PDB 2fdu: Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound

Enzymatic activity of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound

All present enzymatic activity of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound:
1.14.14.1;

Protein crystallography data

The structure of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound, PDB code: 2fdu was solved by J.K.Yano, C.D.Stout, E.F.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.809, 157.698, 103.886, 90.00, 92.23, 90.00
R / Rfree (%) 18.6 / 22.3

Iron Binding Sites:

The binding sites of Iron atom in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound (pdb code 2fdu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound, PDB code: 2fdu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2fdu

Go back to Iron Binding Sites List in 2fdu
Iron binding site 1 out of 4 in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:21.1
occ:1.00
 FE A:HEM500 0.0 21.1 1.0
NC A:HEM500 2.0 20.0 1.0
NA A:HEM500 2.0 18.6 1.0
NB A:HEM500 2.0 19.7 1.0
ND A:HEM500 2.1 20.8 1.0
SG A:CYS439 2.4 20.7 1.0
N_2 A:D1G501 2.4 23.5 1.0
C4A A:HEM500 3.0 19.1 1.0
C1D A:HEM500 3.0 20.1 1.0
C11 A:D1G501 3.0 28.4 1.0
C1C A:HEM500 3.0 19.0 1.0
C4C A:HEM500 3.0 20.0 1.0
C4B A:HEM500 3.0 19.4 1.0
C1B A:HEM500 3.1 17.6 1.0
C4D A:HEM500 3.1 18.9 1.0
C12 A:D1G501 3.1 29.5 1.0
C1A A:HEM500 3.1 19.5 1.0
C10 A:D1G501 3.3 25.6 1.0
CB A:CYS439 3.3 22.1 1.0
CHB A:HEM500 3.3 18.3 1.0
CHD A:HEM500 3.3 19.8 1.0
CHC A:HEM500 3.3 18.0 1.0
CHA A:HEM500 3.4 18.5 1.0
CA A:CYS439 4.2 22.3 1.0
C2C A:HEM500 4.2 20.1 1.0
C2D A:HEM500 4.2 21.6 1.0
C3A A:HEM500 4.2 20.4 1.0
C3C A:HEM500 4.2 20.4 1.0
C3D A:HEM500 4.3 18.7 1.0
C2A A:HEM500 4.3 18.5 1.0
C2B A:HEM500 4.3 18.5 1.0
C3B A:HEM500 4.3 17.8 1.0
C_9 A:D1G501 4.7 25.5 1.0
N A:GLY441 4.9 22.6 1.0
C A:CYS439 4.9 23.8 1.0

Iron binding site 2 out of 4 in 2fdu

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Iron binding site 2 out of 4 in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:24.4
occ:1.00
 FE B:HEM500 0.0 24.4 1.0
NC B:HEM500 2.0 23.7 1.0
NB B:HEM500 2.0 20.6 1.0
ND B:HEM500 2.0 24.3 1.0
NA B:HEM500 2.1 24.0 1.0
SG B:CYS439 2.4 24.8 1.0
N_2 B:D1G501 2.4 30.0 1.0
C1D B:HEM500 3.0 24.0 1.0
C1C B:HEM500 3.0 24.0 1.0
C4B B:HEM500 3.0 22.1 1.0
C4D B:HEM500 3.0 24.0 1.0
C4C B:HEM500 3.0 24.3 1.0
C11 B:D1G501 3.0 33.9 1.0
C1A B:HEM500 3.1 22.7 1.0
C4A B:HEM500 3.1 22.8 1.0
C1B B:HEM500 3.1 22.3 1.0
C12 B:D1G501 3.2 32.6 1.0
CHD B:HEM500 3.3 24.1 1.0
C10 B:D1G501 3.3 33.0 1.0
CHC B:HEM500 3.3 22.3 1.0
CHA B:HEM500 3.4 25.1 1.0
CHB B:HEM500 3.4 22.0 1.0
CB B:CYS439 3.4 24.5 1.0
C2D B:HEM500 4.2 24.9 1.0
C2C B:HEM500 4.2 24.9 1.0
C3D B:HEM500 4.2 25.4 1.0
C3C B:HEM500 4.2 24.1 1.0
CA B:CYS439 4.3 25.7 1.0
C3B B:HEM500 4.3 22.0 1.0
C3A B:HEM500 4.3 22.2 1.0
C2A B:HEM500 4.3 23.9 1.0
C2B B:HEM500 4.3 22.2 1.0
C_9 B:D1G501 4.7 32.5 1.0
N B:GLY441 5.0 29.4 1.0

Iron binding site 3 out of 4 in 2fdu

Go back to Iron Binding Sites List in 2fdu
Iron binding site 3 out of 4 in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:22.8
occ:1.00
 FE C:HEM500 0.0 22.8 1.0
NA C:HEM500 2.0 22.5 1.0
NC C:HEM500 2.1 23.5 1.0
ND C:HEM500 2.1 22.6 1.0
NB C:HEM500 2.1 22.9 1.0
SG C:CYS439 2.3 24.4 1.0
N_2 C:D1G501 2.3 29.3 1.0
C11 C:D1G501 2.9 31.1 1.0
C1D C:HEM500 3.0 21.8 1.0
C1C C:HEM500 3.0 22.2 1.0
C4B C:HEM500 3.0 22.3 1.0
C4D C:HEM500 3.1 21.8 1.0
C4A C:HEM500 3.1 20.2 1.0
C1A C:HEM500 3.1 19.0 1.0
C4C C:HEM500 3.1 23.6 1.0
C12 C:D1G501 3.1 34.1 1.0
C1B C:HEM500 3.1 22.1 1.0
C10 C:D1G501 3.3 31.7 1.0
CHC C:HEM500 3.3 21.9 1.0
CHD C:HEM500 3.4 21.3 1.0
CHA C:HEM500 3.4 19.3 1.0
CB C:CYS439 3.4 21.8 1.0
CHB C:HEM500 3.4 20.0 1.0
CA C:CYS439 4.2 23.4 1.0
C2D C:HEM500 4.2 21.8 1.0
C3D C:HEM500 4.2 21.3 1.0
C2C C:HEM500 4.2 24.9 1.0
C3A C:HEM500 4.2 22.5 1.0
C2A C:HEM500 4.2 20.5 1.0
C3B C:HEM500 4.3 22.9 1.0
C3C C:HEM500 4.3 23.5 1.0
C2B C:HEM500 4.3 21.5 1.0
C_9 C:D1G501 4.6 33.9 1.0
N C:GLY441 4.9 25.2 1.0
C C:CYS439 5.0 24.9 1.0

Iron binding site 4 out of 4 in 2fdu

Go back to Iron Binding Sites List in 2fdu
Iron binding site 4 out of 4 in the Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Microsomal P450 2A6 with the Inhibitor N,N-Dimethyl(5- (Pyridin-3-Yl)Furan-2-Yl)Methanamine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:23.0
occ:1.00
 FE D:HEM500 0.0 23.0 1.0
ND D:HEM500 2.0 23.1 1.0
NC D:HEM500 2.1 22.7 1.0
NB D:HEM500 2.1 21.6 1.0
NA D:HEM500 2.1 20.2 1.0
SG D:CYS439 2.3 24.0 1.0
N_2 D:D1G501 2.4 29.9 1.0
C1D D:HEM500 3.0 22.3 1.0
C11 D:D1G501 3.0 34.1 1.0
C1C D:HEM500 3.0 21.6 1.0
C12 D:D1G501 3.0 35.4 1.0
C1B D:HEM500 3.1 20.1 1.0
C4B D:HEM500 3.1 20.4 1.0
C4D D:HEM500 3.1 20.4 1.0
C4C D:HEM500 3.1 23.2 1.0
C4A D:HEM500 3.1 19.2 1.0
C1A D:HEM500 3.1 21.1 1.0
C10 D:D1G501 3.3 32.3 1.0
CB D:CYS439 3.3 23.1 1.0
CHD D:HEM500 3.3 22.4 1.0
CHC D:HEM500 3.4 21.7 1.0
CHB D:HEM500 3.4 19.4 1.0
CHA D:HEM500 3.4 21.6 1.0
CA D:CYS439 4.2 24.4 1.0
C2C D:HEM500 4.2 21.6 1.0
C2D D:HEM500 4.2 23.3 1.0
C3C D:HEM500 4.3 24.2 1.0
C3D D:HEM500 4.3 22.6 1.0
C3B D:HEM500 4.3 19.8 1.0
C3A D:HEM500 4.3 19.4 1.0
C2B D:HEM500 4.3 21.4 1.0
C2A D:HEM500 4.3 20.2 1.0
C_9 D:D1G501 4.7 34.9 1.0
N D:GLY441 5.0 27.9 1.0
C D:CYS439 5.0 24.8 1.0

Reference:

J.K.Yano, T.T.Denton, M.A.Cerny, X.Zhang, E.F.Johnson, J.R.Cashman. Synthetic Inhibitors of Cytochrome P-450 2A6: Inhibitory Activity, Difference Spectra, Mechanism of Inhibition, and Protein Cocrystallization. J.Med.Chem. V. 49 6987 2006.
ISSN: ISSN 0022-2623
PubMed: 17125252
DOI: 10.1021/JM060519R
Page generated: Thu Jul 17 01:03:17 2025

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