Atomistry » Fluorine » PDB 4x7j-4xxs » 4xvd
Atomistry »
  Fluorine »
    PDB 4x7j-4xxs »
      4xvd »

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

Go back to Fluorine Binding Sites List in 4xvd
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

Go back to Fluorine Binding Sites List in 4xvd
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

Go back to Fluorine Binding Sites List in 4xvd
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy