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Fluorine 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:

Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 8 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 1 out of 8 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 Fluorine with other atoms in the F 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:F490

b:58.8
occ:1.00
 FAE A:JKF490 0.0 58.8 1.0
CAX A:JKF490 1.4 59.0 1.0
CAI A:JKF490 2.4 60.2 1.0
CBC A:JKF490 2.4 56.4 1.0
CBB A:JKF490 2.8 51.4 1.0
CG2 A:VAL461 2.8 36.2 1.0
CBF A:JKF490 3.1 47.1 1.0
CAT A:JKF490 3.1 41.7 1.0
CAB A:JKF490 3.1 35.2 1.0
CAS A:JKF490 3.6 52.7 1.0
CAY A:JKF490 3.7 60.1 1.0
CAH A:JKF490 3.7 59.6 1.0
CD2 A:LEU356 3.9 34.5 1.0
CBG A:JKF490 4.1 47.6 1.0
CBA A:JKF490 4.1 38.0 1.0
CAJ A:JKF490 4.1 59.4 1.0
OAV A:JKF490 4.3 41.2 1.0
O A:HOH484 4.3 39.8 1.0
CB A:VAL461 4.3 37.9 1.0
NBH A:JKF490 4.5 36.5 1.0
CBE A:JKF490 4.5 54.4 1.0
FAF A:JKF490 4.7 66.2 1.0
NBI A:JKF490 4.7 53.8 1.0
CBJ A:JKF490 4.8 36.5 1.0
CAA A:JKF490 4.8 38.8 1.0
O A:PHE290 4.8 38.4 1.0
CG1 A:VAL461 4.9 35.6 1.0
CAQ A:JKF490 4.9 44.3 1.0
N A:VAL461 5.0 38.4 1.0
CAO A:JKF490 5.0 36.8 1.0
CA A:VAL461 5.0 38.0 1.0

Fluorine binding site 2 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 2 out of 8 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 Fluorine with other atoms in the F 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
A:F490

b:66.2
occ:1.00
 FAF A:JKF490 0.0 66.2 1.0
CAY A:JKF490 1.2 60.1 1.0
CAJ A:JKF490 2.3 59.4 1.0
CBC A:JKF490 2.3 56.4 1.0
CBB A:JKF490 2.8 51.4 1.0
SD A:MET106 3.0 65.2 1.0
CE A:MET460 3.0 57.9 1.0
CAS A:JKF490 3.1 52.7 1.0
CZ A:PHE105 3.2 45.5 1.0
CE1 A:PHE105 3.2 41.4 1.0
CAX A:JKF490 3.5 59.0 1.0
CAH A:JKF490 3.5 59.6 1.0
CBF A:JKF490 3.7 47.1 1.0
CG A:MET106 3.8 49.6 1.0
CE A:MET106 3.9 61.8 1.0
CAI A:JKF490 4.0 60.2 1.0
CAT A:JKF490 4.2 41.7 1.0
SD A:MET460 4.3 49.5 1.0
CBE A:JKF490 4.3 54.4 1.0
CD1 A:LEU208 4.4 44.5 1.0
CE2 A:PHE105 4.5 43.2 1.0
CD1 A:PHE105 4.5 43.8 1.0
FAE A:JKF490 4.7 58.8 1.0
CBG A:JKF490 4.7 47.6 1.0
NBI A:JKF490 4.9 53.8 1.0
OAD A:JKF490 5.0 58.2 1.0

Fluorine binding site 3 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 3 out of 8 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 Fluorine with other atoms in the F 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
B:F490

b:57.8
occ:1.00
 FAE B:JKF490 0.0 57.8 1.0
CAX B:JKF490 1.2 53.0 1.0
CBC B:JKF490 2.2 52.8 1.0
CAI B:JKF490 2.2 53.6 1.0
CBB B:JKF490 2.6 50.7 1.0
CG2 B:VAL461 2.9 36.6 1.0
CBF B:JKF490 2.9 45.5 1.0
CAT B:JKF490 3.0 42.3 1.0
CAB B:JKF490 3.1 35.7 1.0
CAY B:JKF490 3.5 56.4 1.0
CAH B:JKF490 3.5 52.5 1.0
CAS B:JKF490 3.6 54.0 1.0
CD2 B:LEU356 3.6 34.1 1.0
CAJ B:JKF490 3.9 55.4 1.0
CBG B:JKF490 4.0 48.6 1.0
CBA B:JKF490 4.1 37.8 1.0
OAV B:JKF490 4.2 36.5 1.0
CB B:VAL461 4.4 39.0 1.0
NBH B:JKF490 4.4 33.6 1.0
FAF B:JKF490 4.4 65.2 1.0
CBE B:JKF490 4.5 55.7 1.0
NBI B:JKF490 4.7 55.3 1.0
CBJ B:JKF490 4.7 35.3 1.0
O B:PHE290 4.8 36.6 1.0
CG B:LEU356 4.9 33.9 1.0
CAQ B:JKF490 4.9 46.9 1.0
CAO B:JKF490 4.9 39.8 1.0
CG1 B:VAL461 5.0 35.4 1.0
CAA B:JKF490 5.0 36.1 1.0

Fluorine binding site 4 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 4 out of 8 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 Fluorine with other atoms in the F 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
B:F490

b:65.2
occ:1.00
 FAF B:JKF490 0.0 65.2 1.0
CAY B:JKF490 1.2 56.4 1.0
CBC B:JKF490 2.2 52.8 1.0
CAJ B:JKF490 2.2 55.4 1.0
CBB B:JKF490 2.7 50.7 1.0
CE B:MET460 2.8 50.8 1.0
CAS B:JKF490 3.1 54.0 1.0
SD B:MET106 3.1 64.9 1.0
CE1 B:PHE105 3.2 40.3 1.0
CZ B:PHE105 3.4 42.8 1.0
CE B:MET106 3.4 64.0 1.0
CAX B:JKF490 3.5 53.0 1.0
CAH B:JKF490 3.5 52.5 1.0
CBF B:JKF490 3.7 45.5 1.0
CAI B:JKF490 4.0 53.6 1.0
CD1 B:LEU208 4.1 39.4 1.0
CG B:MET106 4.2 49.4 1.0
CAT B:JKF490 4.2 42.3 1.0
CBE B:JKF490 4.3 55.7 1.0
CD1 B:PHE105 4.4 36.8 1.0
SD B:MET460 4.4 47.5 1.0
FAE B:JKF490 4.4 57.8 1.0
CE2 B:PHE105 4.7 40.0 1.0
CBG B:JKF490 4.7 48.6 1.0
NBI B:JKF490 4.9 55.3 1.0
OAD B:JKF490 5.0 61.0 1.0

Fluorine binding site 5 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 5 out of 8 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 Fluorine with other atoms in the F binding site number 5 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:F490

b:56.7
occ:1.00
 FAE C:JKF490 0.0 56.7 1.0
CAX C:JKF490 1.3 57.6 1.0
CBC C:JKF490 2.3 55.0 1.0
CAI C:JKF490 2.4 57.9 1.0
CAT C:JKF490 2.7 42.0 1.0
CBB C:JKF490 2.7 51.5 1.0
CAB C:JKF490 2.7 38.1 1.0
CBF C:JKF490 2.9 50.5 1.0
CG2 C:VAL461 3.2 34.3 1.0
CAY C:JKF490 3.6 58.7 1.0
CAH C:JKF490 3.6 57.7 1.0
OAV C:JKF490 3.8 44.1 1.0
CAS C:JKF490 3.8 53.1 1.0
CBA C:JKF490 3.8 43.1 1.0
CD2 C:LEU356 3.8 36.2 1.0
CBG C:JKF490 4.0 49.4 1.0
NBH C:JKF490 4.1 42.3 1.0
O C:HOH486 4.1 45.4 1.0
CAJ C:JKF490 4.1 57.6 1.0
CBJ C:JKF490 4.4 42.2 1.0
CB C:VAL461 4.6 37.1 1.0
O C:PHE290 4.6 40.3 1.0
FAF C:JKF490 4.7 64.1 1.0
CBD C:JKF490 4.7 41.8 1.0
CBE C:JKF490 4.7 54.4 1.0
CAA C:JKF490 4.7 44.4 1.0
CAO C:JKF490 4.7 41.7 1.0
NBI C:JKF490 4.8 52.4 1.0
CAQ C:JKF490 4.8 45.9 1.0
CG1 C:VAL461 5.0 34.4 1.0

Fluorine binding site 6 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 6 out of 8 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 Fluorine with other atoms in the F binding site number 6 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:F490

b:64.1
occ:1.00
 FAF C:JKF490 0.0 64.1 1.0
CAY C:JKF490 1.3 58.7 1.0
CBC C:JKF490 2.3 55.0 1.0
CAJ C:JKF490 2.3 57.6 1.0
CE C:MET460 2.4 54.8 1.0
CBB C:JKF490 2.7 51.5 1.0
CAS C:JKF490 2.8 53.1 1.0
CZ C:PHE105 3.1 47.5 1.0
CE1 C:PHE105 3.3 44.1 1.0
CAX C:JKF490 3.6 57.6 1.0
CAH C:JKF490 3.6 57.7 1.0
CBF C:JKF490 3.9 50.5 1.0
SD C:MET106 4.0 59.7 1.0
CBE C:JKF490 4.0 54.4 1.0
CAI C:JKF490 4.1 57.9 1.0
SD C:MET460 4.2 51.4 1.0
CE2 C:PHE105 4.3 46.2 1.0
CG C:PRO210 4.5 47.4 1.0
CAT C:JKF490 4.5 42.0 1.0
CE C:MET106 4.6 45.5 1.0
OAD C:JKF490 4.6 56.0 1.0
FAE C:JKF490 4.7 56.7 1.0
CB C:MET460 4.7 45.5 1.0
CD1 C:PHE105 4.7 44.2 1.0
CBG C:JKF490 4.8 49.4 1.0
CD1 C:LEU208 4.8 38.1 1.0
NBI C:JKF490 4.8 52.4 1.0
CG C:MET106 4.9 48.7 1.0
CG C:MET460 5.0 46.7 1.0

Fluorine binding site 7 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 7 out of 8 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 Fluorine with other atoms in the F binding site number 7 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:F490

b:52.8
occ:1.00
 FAE D:JKF490 0.0 52.8 1.0
CAX D:JKF490 1.3 51.8 1.0
CAI D:JKF490 2.3 53.0 1.0
CBC D:JKF490 2.4 51.9 1.0
CBB D:JKF490 2.8 46.6 1.0
CG2 D:VAL461 3.0 27.7 1.0
CAB D:JKF490 3.0 23.7 1.0
CAT D:JKF490 3.1 34.9 1.0
CBF D:JKF490 3.1 42.7 1.0
CAH D:JKF490 3.6 54.3 1.0
CAY D:JKF490 3.6 57.2 1.0
CAS D:JKF490 3.7 47.9 1.0
CD2 D:LEU356 3.8 33.1 1.0
CAJ D:JKF490 4.0 56.4 1.0
CBA D:JKF490 4.1 34.4 1.0
CBG D:JKF490 4.2 44.2 1.0
OAV D:JKF490 4.3 34.9 1.0
NBH D:JKF490 4.4 26.5 1.0
O D:HOH561 4.5 37.0 1.0
CB D:VAL461 4.5 30.3 1.0
FAF D:JKF490 4.7 66.2 1.0
CBE D:JKF490 4.7 51.3 1.0
CBJ D:JKF490 4.8 29.6 1.0
NBI D:JKF490 4.9 48.5 1.0
CAA D:JKF490 4.9 33.0 1.0
O D:PHE290 4.9 29.7 1.0
CAO D:JKF490 5.0 34.9 1.0

Fluorine binding site 8 out of 8 in 3tik

Go back to Fluorine Binding Sites List in 3tik
Fluorine binding site 8 out of 8 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 Fluorine with other atoms in the F binding site number 8 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:F490

b:66.2
occ:1.00
 FAF D:JKF490 0.0 66.2 1.0
CAY D:JKF490 1.3 57.2 1.0
CAJ D:JKF490 2.3 56.4 1.0
CBC D:JKF490 2.3 51.9 1.0
CBB D:JKF490 2.8 46.6 1.0
CE D:MET460 2.8 54.3 1.0
CZ D:PHE105 3.0 41.9 1.0
CAS D:JKF490 3.2 47.9 1.0
CE1 D:PHE105 3.2 43.0 1.0
SD D:MET106 3.4 62.4 1.0
CAX D:JKF490 3.5 51.8 1.0
CAH D:JKF490 3.5 54.3 1.0
CBF D:JKF490 3.8 42.7 1.0
CAI D:JKF490 4.0 53.0 1.0
CE D:MET106 4.1 59.0 1.0
CG D:MET106 4.2 49.1 1.0
CAT D:JKF490 4.2 34.9 1.0
CE2 D:PHE105 4.3 43.3 1.0
CBE D:JKF490 4.3 51.3 1.0
CD1 D:LEU208 4.4 39.9 1.0
SD D:MET460 4.5 52.8 1.0
CD1 D:PHE105 4.6 42.8 1.0
FAE D:JKF490 4.7 52.8 1.0
CBG D:JKF490 4.8 44.2 1.0
NBI D:JKF490 5.0 48.5 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 Dec 13 11:55:57 2020

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