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Chlorine in PDB 5ebk: Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine

Enzymatic activity of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine

All present enzymatic activity of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine:
1.8.1.12;

Protein crystallography data

The structure of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine, PDB code: 5ebk was solved by A.Ilari, G.Angiulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 3.51
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 102.500, 102.500, 192.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine (pdb code 5ebk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine, PDB code: 5ebk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5ebk

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Chlorine binding site 1 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:0.2
occ:0.80
 CL A:RDS502 0.0 0.2 0.8
C13 A:RDS502 1.8 0.4 0.8
C12 A:RDS502 2.8 0.7 0.8
C11 A:RDS502 2.8 0.7 0.8
CB A:CYS52 3.2 0.9 1.0
SG A:CYS52 3.2 0.3 1.0
NE2 B:HIS461 3.2 0.7 1.0
SG A:CYS57 3.3 0.7 1.0
OG A:SER14 3.5 0.3 1.0
CG2 A:THR335 3.5 0.9 1.0
CE1 B:HIS461 3.6 0.3 1.0
OG1 A:THR335 3.8 1.0 1.0
CD2 B:HIS461 3.9 0.0 1.0
C8 A:RDS502 4.0 0.1 0.8
C10 A:RDS502 4.1 0.8 0.8
CB A:THR335 4.2 0.1 1.0
CG2 A:VAL53 4.2 0.2 1.0
CB A:SER14 4.2 1.0 1.0
ND1 B:HIS461 4.4 1.0 1.0
CA A:CYS52 4.5 0.0 1.0
N A:VAL53 4.5 0.4 1.0
C A:CYS52 4.5 0.3 1.0
C9 A:RDS502 4.6 0.4 0.8
CG B:HIS461 4.6 0.9 1.0

Chlorine binding site 2 out of 7 in 5ebk

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Chlorine binding site 2 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:0.7
occ:0.80
 CL A:RDS503 0.0 0.7 0.8
C13 A:RDS503 1.8 0.4 0.8
NH2 A:ARG228 2.7 0.6 1.0
C11 A:RDS503 2.8 0.7 0.8
C12 A:RDS503 2.8 0.1 0.8
CZ A:ARG228 3.6 0.1 1.0
OH A:TYR221 3.9 0.6 1.0
CB A:ARG228 4.0 0.0 1.0
C10 A:RDS503 4.1 0.2 0.8
C8 A:RDS503 4.1 0.9 0.8
NH1 A:ARG228 4.2 1.0 1.0
NE A:ARG228 4.5 0.2 1.0
C9 A:RDS503 4.6 0.0 0.8
N A:ARG228 4.8 0.7 1.0
CA A:ARG228 4.8 0.8 1.0

Chlorine binding site 3 out of 7 in 5ebk

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Chlorine binding site 3 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:0.6
occ:0.80
 CL A:RDS504 0.0 0.6 0.8
C13 A:RDS504 1.8 0.0 0.8
C11 A:RDS504 2.8 0.5 0.8
C12 A:RDS504 2.8 0.6 0.8
O A:ARG222 3.2 0.8 1.0
OD1 A:ASN252 3.4 0.6 1.0
CB A:ASN252 3.7 0.9 1.0
CA A:ASN252 3.9 0.4 1.0
CG A:ASN252 4.0 0.4 1.0
C10 A:RDS504 4.1 0.6 0.8
C8 A:RDS504 4.1 0.9 0.8
C A:ASN252 4.2 0.7 1.0
C A:ARG222 4.3 0.1 1.0
O A:ASN252 4.4 0.6 1.0
C9 A:RDS504 4.6 0.9 0.8
CA A:ARG222 4.9 0.2 1.0
N A:LEU253 4.9 0.6 1.0
N2 A:RDS504 5.0 0.9 0.8

Chlorine binding site 4 out of 7 in 5ebk

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Chlorine binding site 4 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:0.1
occ:0.80
 CL B:RDS501 0.0 0.1 0.8
C13 B:RDS501 1.8 0.1 0.8
C11 B:RDS501 2.8 0.1 0.8
C12 B:RDS501 2.8 0.5 0.8
OE1 B:GLU467 2.8 0.0 1.0
CD2 B:PHE396 3.2 1.0 1.0
CE2 B:PHE396 3.4 0.1 1.0
C1 A:RDS502 3.4 0.3 0.8
CG B:PHE396 3.5 0.1 1.0
O A:RDS502 3.5 0.3 0.8
CD B:GLU467 3.6 0.4 1.0
C2 A:RDS502 3.6 0.2 0.8
CZ B:PHE396 3.9 0.5 1.0
CD1 B:PHE396 4.0 0.9 1.0
C10 B:RDS501 4.1 0.8 0.8
C8 B:RDS501 4.1 0.9 0.8
CB B:PHE396 4.1 0.7 1.0
CE1 B:PHE396 4.2 1.0 1.0
CG B:GLU467 4.3 0.2 1.0
C A:RDS502 4.3 0.1 0.8
OE2 B:GLU467 4.3 0.4 1.0
CB B:GLU467 4.5 0.9 1.0
C9 B:RDS501 4.6 0.9 0.8
N1 A:RDS502 4.6 0.3 0.8
N A:RDS502 4.8 0.4 0.8
C3 A:RDS502 4.8 0.2 0.8
N1 B:RDS501 4.8 0.9 0.8
C4 A:RDS502 5.0 0.4 0.8

Chlorine binding site 5 out of 7 in 5ebk

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Chlorine binding site 5 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:98.0
occ:1.00
 CL B:RDS503 0.0 98.0 1.0
C13 B:RDS503 1.8 0.7 1.0
NE2 A:HIS461 2.4 0.1 1.0
SG B:CYS57 2.5 0.4 1.0
SG B:CYS52 2.6 0.0 1.0
C12 B:RDS503 2.8 0.3 1.0
C11 B:RDS503 2.8 0.4 1.0
CB B:CYS52 3.0 0.2 1.0
CE1 A:HIS461 3.1 0.6 1.0
CD2 A:HIS461 3.1 0.6 1.0
CG2 B:THR335 3.6 0.7 1.0
OG1 B:THR335 3.7 0.2 1.0
ND1 A:HIS461 3.9 0.5 1.0
CG A:HIS461 3.9 0.9 1.0
CB B:THR335 4.0 0.4 1.0
C8 B:RDS503 4.0 0.4 1.0
C10 B:RDS503 4.1 0.5 1.0
CB B:CYS57 4.1 0.2 1.0
OG B:SER14 4.1 0.4 1.0
CA B:CYS52 4.3 0.4 1.0
C B:CYS52 4.4 0.9 1.0
C9 B:RDS503 4.6 0.1 1.0
N B:VAL53 4.6 0.7 1.0
CG2 B:VAL53 4.8 1.0 1.0
O B:CYS52 4.8 99.6 1.0
CB B:SER14 4.9 0.9 1.0

Chlorine binding site 6 out of 7 in 5ebk

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Chlorine binding site 6 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:0.8
occ:0.80
 CL B:RDS504 0.0 0.8 0.8
C13 B:RDS504 1.8 0.6 0.8
C11 B:RDS504 2.8 0.6 0.8
C12 B:RDS504 2.8 0.5 0.8
NH2 B:ARG228 3.1 0.1 1.0
CZ B:ARG228 3.9 0.9 1.0
C10 B:RDS504 4.1 0.8 0.8
C8 B:RDS504 4.1 0.7 0.8
CB B:ARG228 4.1 0.1 1.0
NE B:ARG228 4.3 0.7 1.0
OH B:TYR221 4.6 0.4 1.0
C9 B:RDS504 4.6 0.8 0.8
O B:ARG228 4.7 0.1 1.0
NH1 B:ARG228 4.8 0.3 1.0
N B:ARG228 4.9 0.7 1.0
CA B:ARG228 4.9 0.7 1.0

Chlorine binding site 7 out of 7 in 5ebk

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Chlorine binding site 7 out of 7 in the Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Trypanothione Reductase in Complex with 6-(Sec-Butoxy)-2-((3- Chlorophenyl)Thio)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:0.5
occ:0.80
 CL B:RDS505 0.0 0.5 0.8
C13 B:RDS505 1.8 0.1 0.8
C11 B:RDS505 2.8 0.1 0.8
C12 B:RDS505 2.8 0.8 0.8
O B:ARG222 3.4 0.6 1.0
OD1 B:ASN252 3.6 0.8 1.0
CB B:ASN252 3.8 0.3 1.0
CA B:ASN252 4.0 0.5 1.0
C10 B:RDS505 4.1 0.2 0.8
C8 B:RDS505 4.1 0.3 0.8
CG B:ASN252 4.2 0.6 1.0
C B:ASN252 4.3 0.2 1.0
O B:ASN252 4.5 0.5 1.0
C B:ARG222 4.5 0.5 1.0
C9 B:RDS505 4.6 0.9 0.8

Reference:

F.Saccoliti, G.Angiulli, G.Pupo, L.Pescatori, V.N.Madia, A.Messore, G.Colotti, A.Fiorillo, L.Scipione, M.Gramiccia, T.Di Muccio, R.Di Santo, R.Costi, A.Ilari. Inhibition of Leishmania Infantum Trypanothione Reductase By Diaryl Sulfide Derivatives. J Enzyme Inhib Med Chem V. 32 304 2017.
ISSN: ESSN 1475-6374
PubMed: 28098499
DOI: 10.1080/14756366.2016.1250755
Page generated: Sat Jul 12 01:37:22 2025

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