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Fluorine in PDB 3hok: X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode

Enzymatic activity of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode

All present enzymatic activity of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode:
1.14.99.3;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode, PDB code: 3hok was solved by M.N.Rahman, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.072, 54.592, 71.884, 90.00, 94.64, 90.00
R / Rfree (%) 22.2 / 28.9

Other elements in 3hok:

The structure of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode (pdb code 3hok). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode, PDB code: 3hok:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3hok

Go back to Fluorine Binding Sites List in 3hok
Fluorine binding site 1 out of 3 in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:60.6
occ:1.00
 FBD B:Q80301 0.0 60.6 1.0
CBB B:Q80301 1.3 60.9 1.0
FBE B:Q80301 2.2 60.5 1.0
FBC B:Q80301 2.2 61.7 1.0
CAY B:Q80301 2.3 61.0 1.0
CAX B:Q80301 2.7 61.3 1.0
CB B:ARG35 3.5 33.7 1.0
CAZ B:Q80301 3.6 60.1 1.0
CG B:ARG35 3.6 35.5 1.0
CD B:ARG35 3.6 36.3 1.0
O B:ALA31 3.8 35.2 1.0
OE1 B:GLU32 3.9 36.8 1.0
C B:ALA31 4.0 34.8 1.0
NAW B:Q80301 4.0 61.4 1.0
CA B:GLU32 4.0 33.7 1.0
N B:GLU32 4.1 34.3 1.0
O B:HOH254 4.3 57.0 1.0
CB B:ALA31 4.5 35.2 1.0
CB B:PHE214 4.5 36.4 1.0
CBA B:Q80301 4.7 59.9 1.0
NH1 B:ARG35 4.7 37.5 1.0
CB B:GLU32 4.7 33.8 1.0
O B:PHE214 4.8 35.6 1.0
CAV B:Q80301 4.8 60.3 1.0
CA B:ALA31 4.9 35.2 1.0
NE B:ARG35 4.9 37.6 1.0
CD B:GLU32 4.9 34.7 1.0
C B:PHE214 4.9 35.8 1.0
CA B:ARG35 4.9 34.2 1.0

Fluorine binding site 2 out of 3 in 3hok

Go back to Fluorine Binding Sites List in 3hok
Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:60.5
occ:1.00
 FBE B:Q80301 0.0 60.5 1.0
CBB B:Q80301 1.3 60.9 1.0
FBC B:Q80301 2.1 61.7 1.0
FBD B:Q80301 2.2 60.6 1.0
CAY B:Q80301 2.2 61.0 1.0
CB B:PHE214 2.8 36.4 1.0
C B:PHE214 2.9 35.8 1.0
CAZ B:Q80301 3.0 60.1 1.0
CAX B:Q80301 3.1 61.3 1.0
O B:PHE214 3.2 35.6 1.0
N B:GLU215 3.2 36.4 1.0
CA B:PHE214 3.4 35.9 1.0
CA B:GLU215 3.9 36.7 1.0
CG B:PHE214 4.2 38.5 1.0
CBA B:Q80301 4.2 59.9 1.0
NAW B:Q80301 4.3 61.4 1.0
CG B:GLU215 4.4 38.4 1.0
N B:PHE214 4.5 34.6 1.0
O B:ILE211 4.6 31.8 1.0
CAV B:Q80301 4.7 60.3 1.0
CB B:GLU215 4.8 36.7 1.0
CD2 B:PHE214 4.8 40.4 1.0
O B:HOH254 5.0 57.0 1.0
CB B:ALA31 5.0 35.2 1.0

Fluorine binding site 3 out of 3 in 3hok

Go back to Fluorine Binding Sites List in 3hok
Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:61.7
occ:1.00
 FBC B:Q80301 0.0 61.7 1.0
CBB B:Q80301 1.3 60.9 1.0
FBE B:Q80301 2.1 60.5 1.0
FBD B:Q80301 2.2 60.6 1.0
CAY B:Q80301 2.3 61.0 1.0
CAZ B:Q80301 2.8 60.1 1.0
CB B:ALA31 2.9 35.2 1.0
CAX B:Q80301 3.5 61.3 1.0
C B:ALA31 3.7 34.8 1.0
O B:ALA31 3.8 35.2 1.0
CA B:ALA31 3.8 35.2 1.0
CBA B:Q80301 4.1 59.9 1.0
N B:GLU32 4.2 34.3 1.0
CG B:GLU215 4.3 38.4 1.0
N B:GLU215 4.6 36.4 1.0
CB B:PHE214 4.6 36.4 1.0
NAW B:Q80301 4.6 61.4 1.0
CA B:GLU32 4.8 33.7 1.0
C B:PHE214 4.8 35.8 1.0
CAV B:Q80301 4.9 60.3 1.0
CB B:ARG35 4.9 33.7 1.0
CA B:GLU215 4.9 36.7 1.0

Reference:

M.N.Rahman, J.Z.Vlahakis, D.Vukomanovic, W.A.Szarek, K.Nakatsu, Z.Jia. X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R,4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H- Imidazol-1-Yl)Methyl]-4[((5-Trifluoromethylpyridin- 2-Yl)Thio)Methyl]-1,3-Dioxolane: A Novel, Inducible Binding Mode. J.Med.Chem. V. 52 4946 2009.
ISSN: ISSN 0022-2623
PubMed: 19601578
DOI: 10.1021/JM900434F
Page generated: Wed Jul 31 19:21:39 2024

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