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Iron in PDB 3tik: Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One

Enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One

All present enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One:
1.14.13.70;

Protein crystallography data

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One, PDB code: 3tik was solved by T.Y.Hargrove, Z.Wawrzak, J.M.Kraus, M.H.Gelb, F.S.Buckner, M.R.Waterman, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.722, 79.715, 117.521, 74.47, 81.58, 68.05
R / Rfree (%) 18.6 / 24.3

Other elements in 3tik:

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One (pdb code 3tik). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One, PDB code: 3tik:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3tik

Go back to Iron Binding Sites List in 3tik
Iron binding site 1 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe482

b:33.1
occ:1.00
 FE A:HEM482 0.0 33.1 1.0
NA A:HEM482 2.0 32.5 1.0
NB A:HEM482 2.0 29.1 1.0
NC A:HEM482 2.0 32.0 1.0
ND A:HEM482 2.1 31.5 1.0
NAU A:JKF490 2.1 37.0 1.0
SG A:CYS422 2.3 35.0 1.0
CAR A:JKF490 3.0 33.6 1.0
C4A A:HEM482 3.0 33.4 1.0
C4C A:HEM482 3.0 34.0 1.0
C1A A:HEM482 3.0 31.9 1.0
C4B A:HEM482 3.0 30.4 1.0
C1B A:HEM482 3.0 33.1 1.0
C1D A:HEM482 3.0 32.6 1.0
C4D A:HEM482 3.1 34.4 1.0
C1C A:HEM482 3.1 34.4 1.0
CAP A:JKF490 3.1 33.7 1.0
CB A:CYS422 3.4 32.4 1.0
CHD A:HEM482 3.4 32.1 1.0
CHB A:HEM482 3.4 31.6 1.0
CHA A:HEM482 3.4 31.7 1.0
CHC A:HEM482 3.4 32.6 1.0
CA A:CYS422 4.0 34.2 1.0
NBH A:JKF490 4.1 36.5 1.0
CBD A:JKF490 4.2 36.3 1.0
C3A A:HEM482 4.2 34.1 1.0
C2A A:HEM482 4.2 31.7 1.0
C3B A:HEM482 4.3 31.4 1.0
C3C A:HEM482 4.3 36.3 1.0
C2B A:HEM482 4.3 32.7 1.0
C2D A:HEM482 4.3 32.4 1.0
C3D A:HEM482 4.3 33.9 1.0
C2C A:HEM482 4.3 34.9 1.0
CB A:ALA291 4.8 35.6 1.0
N A:GLY424 4.8 35.8 1.0
C A:CYS422 4.8 34.0 1.0
N A:ILE423 4.9 33.5 1.0

Iron binding site 2 out of 4 in 3tik

Go back to Iron Binding Sites List in 3tik
Iron binding site 2 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe482

b:31.0
occ:1.00
 FE B:HEM482 0.0 31.0 1.0
NC B:HEM482 2.0 31.0 1.0
NB B:HEM482 2.0 27.8 1.0
NA B:HEM482 2.0 30.4 1.0
NAU B:JKF490 2.1 34.1 1.0
ND B:HEM482 2.1 30.8 1.0
SG B:CYS422 2.3 30.8 1.0
C4C B:HEM482 3.0 31.4 1.0
C1B B:HEM482 3.0 27.6 1.0
C1D B:HEM482 3.0 31.9 1.0
CAP B:JKF490 3.0 33.6 1.0
CAR B:JKF490 3.0 31.7 1.0
C4A B:HEM482 3.0 25.0 1.0
C4B B:HEM482 3.0 30.6 1.0
C1C B:HEM482 3.1 30.2 1.0
C4D B:HEM482 3.1 31.4 1.0
C1A B:HEM482 3.1 25.6 1.0
CHD B:HEM482 3.4 30.1 1.0
CHB B:HEM482 3.4 23.9 1.0
CB B:CYS422 3.4 30.6 1.0
CHC B:HEM482 3.4 33.1 1.0
CHA B:HEM482 3.5 27.7 1.0
CA B:CYS422 4.1 33.0 1.0
CBD B:JKF490 4.1 33.6 1.0
NBH B:JKF490 4.2 33.6 1.0
C3C B:HEM482 4.2 34.0 1.0
C2B B:HEM482 4.2 30.2 1.0
C3B B:HEM482 4.3 31.4 1.0
C2C B:HEM482 4.3 32.6 1.0
C2D B:HEM482 4.3 32.2 1.0
C3A B:HEM482 4.3 27.2 1.0
C2A B:HEM482 4.3 29.3 1.0
C3D B:HEM482 4.3 32.6 1.0
CB B:ALA291 4.7 32.4 1.0
N B:GLY424 4.8 28.2 1.0
N B:ILE423 4.8 31.6 1.0
C B:CYS422 4.9 32.1 1.0

Iron binding site 3 out of 4 in 3tik

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Iron binding site 3 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe482

b:39.0
occ:1.00
 FE C:HEM482 0.0 39.0 1.0
NC C:HEM482 2.0 36.7 1.0
NB C:HEM482 2.0 37.2 1.0
NA C:HEM482 2.0 39.5 1.0
ND C:HEM482 2.1 39.9 1.0
NAU C:JKF490 2.1 42.3 1.0
SG C:CYS422 2.3 41.7 1.0
CAR C:JKF490 3.0 38.9 1.0
C4C C:HEM482 3.0 40.2 1.0
C4B C:HEM482 3.0 37.2 1.0
C1C C:HEM482 3.0 38.3 1.0
C1D C:HEM482 3.0 41.9 1.0
C4A C:HEM482 3.0 37.8 1.0
C1B C:HEM482 3.1 37.5 1.0
C4D C:HEM482 3.1 41.1 1.0
C1A C:HEM482 3.1 41.0 1.0
CAP C:JKF490 3.1 40.7 1.0
CB C:CYS422 3.3 41.0 1.0
CHD C:HEM482 3.4 38.8 1.0
CHC C:HEM482 3.4 38.0 1.0
CHB C:HEM482 3.4 38.3 1.0
CHA C:HEM482 3.5 41.0 1.0
CA C:CYS422 4.1 43.5 1.0
NBH C:JKF490 4.1 42.3 1.0
CBD C:JKF490 4.2 41.8 1.0
C3C C:HEM482 4.2 41.6 1.0
C3B C:HEM482 4.3 37.5 1.0
C2C C:HEM482 4.3 40.7 1.0
C3A C:HEM482 4.3 36.7 1.0
C2B C:HEM482 4.3 39.1 1.0
C2D C:HEM482 4.3 45.5 1.0
C3D C:HEM482 4.3 43.4 1.0
C2A C:HEM482 4.3 39.8 1.0
N C:GLY424 4.7 43.2 1.0
CB C:ALA291 4.8 36.5 1.0
C C:CYS422 4.8 43.2 1.0
N C:ILE423 4.8 42.4 1.0

Iron binding site 4 out of 4 in 3tik

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Iron binding site 4 out of 4 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Tipifarnib Derivative 6-((4-Chlorophenyl)(Methoxy)(1-Methyl- 1H-Imidazol-5-Yl)Methyl)-4-(2,6-Difluorophenyl)-1-Methylquinolin- 2(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe482

b:27.7
occ:1.00
 FE D:HEM482 0.0 27.7 1.0
NB D:HEM482 2.0 25.8 1.0
NC D:HEM482 2.0 25.7 1.0
NA D:HEM482 2.0 25.7 1.0
ND D:HEM482 2.0 27.7 1.0
NAU D:JKF490 2.2 26.7 1.0
SG D:CYS422 2.3 29.1 1.0
C4A D:HEM482 3.0 26.6 1.0
C4C D:HEM482 3.0 28.1 1.0
C4B D:HEM482 3.0 24.8 1.0
C1B D:HEM482 3.0 24.6 1.0
C4D D:HEM482 3.1 30.0 1.0
C1D D:HEM482 3.1 30.6 1.0
C1C D:HEM482 3.1 24.2 1.0
C1A D:HEM482 3.1 26.0 1.0
CAR D:JKF490 3.1 21.8 1.0
CAP D:JKF490 3.2 25.6 1.0
CB D:CYS422 3.4 27.6 1.0
CHB D:HEM482 3.4 24.2 1.0
CHA D:HEM482 3.4 28.8 1.0
CHD D:HEM482 3.4 29.7 1.0
CHC D:HEM482 3.4 25.1 1.0
CA D:CYS422 4.0 29.5 1.0
NBH D:JKF490 4.2 26.5 1.0
C3B D:HEM482 4.2 23.6 1.0
C3C D:HEM482 4.3 27.9 1.0
C3A D:HEM482 4.3 26.0 1.0
CBD D:JKF490 4.3 26.1 1.0
C2B D:HEM482 4.3 23.0 1.0
C2C D:HEM482 4.3 26.8 1.0
C2A D:HEM482 4.3 24.6 1.0
C3D D:HEM482 4.3 31.2 1.0
C2D D:HEM482 4.3 31.8 1.0
CB D:ALA291 4.7 26.0 1.0
N D:GLY424 4.8 29.6 1.0
C D:CYS422 4.8 29.7 1.0
N D:ILE423 4.8 31.2 1.0

Reference:

F.S.Buckner, M.T.Bahia, P.K.Suryadevara, K.L.White, D.M.Shackleford, N.K.Chennamaneni, M.A.Hulverson, J.U.Laydbak, E.Chatelain, I.Scandale, C.L.Verlinde, S.A.Charman, G.I.Lepesheva, M.H.Gelb. Pharmacological Characterization, Structural Studies, and in Vivo Activities of Anti-Chagas Disease Lead Compounds Derived From Tipifarnib. Antimicrob.Agents Chemother. V. 56 4914 2012.
ISSN: ISSN 0066-4804
PubMed: 22777048
DOI: 10.1128/AAC.06244-11
Page generated: Sun Aug 4 20:28:30 2024

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