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Fluorine in PDB 4xvd: 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol

Enzymatic activity of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol

All present enzymatic activity of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol:
1.1.1.64;

Protein crystallography data

The structure of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol, PDB code: 4xvd was solved by Y.Amano, T.Yamaguchi, T.Niimi, H.Sakashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.67 / 2.81
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 145.795, 145.795, 74.287, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol (pdb code 4xvd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol, PDB code: 4xvd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4xvd

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Fluorine binding site 1 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:18.4
occ:1.00
 F14 A:WDV402 0.0 18.4 1.0
C12 A:WDV402 1.3 18.4 1.0
F15 A:WDV402 2.1 18.8 1.0
F16 A:WDV402 2.2 19.4 1.0
C7 A:WDV402 2.3 17.7 1.0
C11 A:WDV402 2.9 16.8 1.0
O A:PHE306 3.0 22.2 1.0
C A:PHE306 3.4 23.7 1.0
C3 A:WDV402 3.5 17.9 1.0
CA A:ASN307 3.5 29.1 1.0
CE1 A:TYR317 3.6 21.1 1.0
N A:ASN307 3.6 26.8 1.0
OH A:TYR317 3.8 23.0 1.0
C A:ASN307 4.0 31.1 1.0
N A:SER308 4.0 31.6 1.0
CE2 A:TYR319 4.1 22.0 1.0
CZ A:TYR317 4.2 21.7 1.0
C8 A:WDV402 4.2 16.5 1.0
ND1 A:HIS304 4.2 19.5 1.0
CE1 A:HIS304 4.2 19.9 1.0
CB A:PHE306 4.3 22.3 1.0
CD2 A:TYR319 4.3 22.5 1.0
CA A:PHE306 4.5 22.9 1.0
C1 A:WDV402 4.6 18.6 1.0
CD1 A:TYR317 4.8 21.6 1.0
O A:ASN307 4.8 31.6 1.0
CB A:ASN307 4.9 30.1 1.0
CB A:SER308 4.9 32.1 1.0
C4 A:WDV402 4.9 17.3 1.0

Fluorine binding site 2 out of 6 in 4xvd

Go back to Fluorine Binding Sites List in 4xvd
Fluorine binding site 2 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:18.8
occ:1.00
 F15 A:WDV402 0.0 18.8 1.0
C12 A:WDV402 1.4 18.4 1.0
F14 A:WDV402 2.1 18.4 1.0
F16 A:WDV402 2.2 19.4 1.0
C7 A:WDV402 2.4 17.7 1.0
C3 A:WDV402 2.7 17.9 1.0
C A:ASN307 3.1 31.1 1.0
N A:ASN307 3.2 26.8 1.0
CE3 A:TRP227 3.3 26.6 1.0
CA A:ASN307 3.3 29.1 1.0
CZ3 A:TRP227 3.4 26.7 1.0
N A:SER308 3.4 31.6 1.0
O A:ASN307 3.4 31.6 1.0
C A:PHE306 3.5 23.7 1.0
C11 A:WDV402 3.7 16.8 1.0
CB A:SER308 3.7 32.1 1.0
O A:PHE306 3.8 22.2 1.0
CB A:PHE306 4.0 22.3 1.0
C1 A:WDV402 4.1 18.6 1.0
CA A:SER308 4.1 30.9 1.0
CA A:PHE306 4.3 22.9 1.0
CD2 A:TRP227 4.5 25.9 1.0
C5 A:WDV402 4.5 19.8 1.0
CH2 A:TRP227 4.6 25.5 1.0
C8 A:WDV402 4.8 16.5 1.0
CB A:ASN307 4.8 30.1 1.0
OG A:SER308 4.8 34.7 1.0
N2 A:WDV402 4.9 20.0 1.0
C4 A:WDV402 4.9 17.3 1.0
CB A:PHE311 5.0 24.7 1.0

Fluorine binding site 3 out of 6 in 4xvd

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Fluorine binding site 3 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:19.4
occ:1.00
 F16 A:WDV402 0.0 19.4 1.0
C12 A:WDV402 1.4 18.4 1.0
F15 A:WDV402 2.2 18.8 1.0
F14 A:WDV402 2.2 18.4 1.0
C7 A:WDV402 2.4 17.7 1.0
C11 A:WDV402 3.1 16.8 1.0
CE1 A:TYR317 3.2 21.1 1.0
C3 A:WDV402 3.3 17.9 1.0
CB A:PHE311 3.5 24.7 1.0
CB A:SER308 3.7 32.1 1.0
CD1 A:TYR317 3.8 21.6 1.0
N A:SER308 4.0 31.6 1.0
CZ A:TYR317 4.3 21.7 1.0
C8 A:WDV402 4.3 16.5 1.0
C A:ASN307 4.4 31.1 1.0
CA A:SER308 4.4 30.9 1.0
C1 A:WDV402 4.5 18.6 1.0
O A:SER308 4.5 34.3 1.0
CG A:PHE311 4.5 24.2 1.0
C A:PHE311 4.5 24.9 1.0
OH A:TYR317 4.5 23.0 1.0
CZ3 A:TRP227 4.6 26.7 1.0
CE A:MET120 4.6 21.8 1.0
CA A:PHE311 4.6 25.4 1.0
N A:ALA312 4.6 23.9 1.0
CA A:ASN307 4.7 29.1 1.0
SD A:MET120 4.7 23.4 1.0
O A:PHE311 4.9 24.4 1.0
C4 A:WDV402 4.9 17.3 1.0
OG A:SER308 4.9 34.7 1.0
CD2 A:PHE311 4.9 23.3 1.0
C A:SER308 4.9 32.7 1.0
O A:ASN307 5.0 31.6 1.0

Fluorine binding site 4 out of 6 in 4xvd

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Fluorine binding site 4 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:41.9
occ:1.00
 F14 B:WDV402 0.0 41.9 1.0
C12 B:WDV402 1.4 39.2 1.0
F16 B:WDV402 2.1 40.1 1.0
F15 B:WDV402 2.3 37.7 1.0
C7 B:WDV402 2.4 37.4 1.0
O B:PHE306 2.7 39.8 1.0
C11 B:WDV402 3.0 35.4 1.0
C B:PHE306 3.3 46.2 1.0
OH B:TYR317 3.4 38.3 1.0
CA B:ASN307 3.5 53.5 1.0
C3 B:WDV402 3.5 36.8 1.0
N B:ASN307 3.6 49.1 1.0
CE1 B:TYR317 3.7 33.7 1.0
C B:ASN307 3.9 53.8 1.0
CZ B:TYR317 4.0 35.9 1.0
ND1 B:HIS304 4.0 53.6 1.0
CE2 B:TYR319 4.1 38.8 1.0
N B:SER308 4.1 53.8 1.0
CE1 B:HIS304 4.2 56.0 1.0
C8 B:WDV402 4.3 34.2 1.0
CB B:PHE306 4.3 42.0 1.0
CD2 B:TYR319 4.4 39.4 1.0
CA B:PHE306 4.4 45.9 1.0
O B:ASN307 4.7 51.3 1.0
C1 B:WDV402 4.7 37.1 1.0
CB B:ASN307 4.9 57.6 1.0
ND2 B:ASN307 4.9 62.5 1.0
CB B:SER308 4.9 54.6 1.0
CD1 B:TYR317 5.0 33.9 1.0
C4 B:WDV402 5.0 35.5 1.0

Fluorine binding site 5 out of 6 in 4xvd

Go back to Fluorine Binding Sites List in 4xvd
Fluorine binding site 5 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:37.7
occ:1.00
 F15 B:WDV402 0.0 37.7 1.0
C12 B:WDV402 1.4 39.2 1.0
F16 B:WDV402 2.2 40.1 1.0
F14 B:WDV402 2.3 41.9 1.0
C7 B:WDV402 2.3 37.4 1.0
C3 B:WDV402 2.6 36.8 1.0
CZ3 B:TRP227 3.2 44.1 1.0
CE3 B:TRP227 3.3 47.3 1.0
C B:ASN307 3.3 53.8 1.0
N B:ASN307 3.5 49.1 1.0
O B:ASN307 3.5 51.3 1.0
CA B:ASN307 3.6 53.5 1.0
C11 B:WDV402 3.6 35.4 1.0
N B:SER308 3.7 53.8 1.0
C B:PHE306 3.7 46.2 1.0
CB B:SER308 3.7 54.6 1.0
O B:PHE306 3.9 39.8 1.0
C1 B:WDV402 4.0 37.1 1.0
CB B:PHE306 4.1 42.0 1.0
CA B:SER308 4.3 55.4 1.0
CH2 B:TRP227 4.4 43.5 1.0
CA B:PHE306 4.5 45.9 1.0
CD2 B:TRP227 4.5 47.5 1.0
C5 B:WDV402 4.5 36.9 1.0
C8 B:WDV402 4.7 34.2 1.0
CB B:PHE311 4.8 48.7 1.0
N2 B:WDV402 4.8 37.0 1.0
OG B:SER308 4.8 57.7 1.0
C4 B:WDV402 4.9 35.5 1.0
CE1 B:TYR317 4.9 33.7 1.0

Fluorine binding site 6 out of 6 in 4xvd

Go back to Fluorine Binding Sites List in 4xvd
Fluorine binding site 6 out of 6 in the 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 17BETA-HSD5 in Complex with 4-Nitro-2-({4-[3-(Trifluoromethyl) Phenyl]Piperazin-1-Yl}Methyl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:40.1
occ:1.00
 F16 B:WDV402 0.0 40.1 1.0
C12 B:WDV402 1.4 39.2 1.0
F14 B:WDV402 2.1 41.9 1.0
F15 B:WDV402 2.2 37.7 1.0
C7 B:WDV402 2.4 37.4 1.0
CE1 B:TYR317 2.8 33.7 1.0
C11 B:WDV402 3.0 35.4 1.0
C3 B:WDV402 3.4 36.8 1.0
OH B:TYR317 3.7 38.3 1.0
CZ B:TYR317 3.7 35.9 1.0
CD1 B:TYR317 3.7 33.9 1.0
CB B:PHE311 3.7 48.7 1.0
CB B:SER308 3.9 54.6 1.0
N B:SER308 4.2 53.8 1.0
C8 B:WDV402 4.3 34.2 1.0
C B:ASN307 4.4 53.8 1.0
C1 B:WDV402 4.6 37.1 1.0
CA B:SER308 4.6 55.4 1.0
C B:PHE311 4.7 46.7 1.0
CG B:PHE311 4.7 50.8 1.0
CA B:ASN307 4.7 53.5 1.0
N B:ALA312 4.7 45.8 1.0
O B:PHE306 4.7 39.8 1.0
CA B:PHE311 4.8 49.9 1.0
CZ3 B:TRP227 4.8 44.1 1.0
SD B:MET120 4.8 32.5 1.0
CE B:MET120 4.9 31.4 1.0
O B:SER308 4.9 66.8 1.0
C4 B:WDV402 4.9 35.5 1.0

Reference:

Y.Amano, T.Yamaguchi, T.Niimi, H.Sakashita. Structures of Complexes of Type 5 17 Beta-Hydroxysteroid Dehydrogenase with Structurally Diverse Inhibitors: Insights Into the Conformational Changes Upon Inhibitor Binding Acta Crystallogr.,Sect.D V. 71 918 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004715002175
Page generated: Thu Aug 1 06:49:44 2024

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