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Chlorine in PDB 7eri: Crystal Structure of V30M-Ttr in Complex with Triclabendazole

Protein crystallography data

The structure of Crystal Structure of V30M-Ttr in Complex with Triclabendazole, PDB code: 7eri was solved by T.Yokoyama, M.Kashihara, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.64 / 1.81
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.993, 85.226, 63.727, 90, 90, 90
R / Rfree (%) 18.9 / 22.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole (pdb code 7eri). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole, PDB code: 7eri:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7eri

Go back to Chlorine Binding Sites List in 7eri
Chlorine binding site 1 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:32.1
occ:0.50
 CLQ A:JA9201 0.0 32.1 0.5
CAI A:JA9201 1.6 31.5 0.5
CAK A:JA9201 2.6 33.5 0.5
CAH A:JA9201 2.6 30.1 0.5
OAG A:JA9201 2.8 31.0 0.5
CAB A:JA9201 3.1 29.0 0.5
O A:ALA109 3.3 18.7 1.0
CAD A:JA9201 3.5 26.9 0.5
C A:ALA109 3.6 20.6 1.0
CLU A:JA9201 3.8 29.7 0.5
CG A:LEU17 3.8 23.3 1.0
CD1 A:LEU17 3.8 24.1 1.0
N A:ALA109 3.8 16.7 1.0
CAM A:JA9201 3.8 35.5 0.5
CAA A:JA9201 3.9 29.9 0.5
CAJ A:JA9201 3.9 32.8 0.5
CB A:ALA108 4.0 22.2 1.0
N A:LEU110 4.1 15.8 1.0
CB A:LEU110 4.2 15.5 1.0
CB A:LEU17 4.2 16.2 1.0
CA A:ALA109 4.3 18.0 1.0
CA A:LEU110 4.3 15.9 1.0
C A:ALA108 4.3 21.0 1.0
CAL A:JA9201 4.4 34.5 0.5
CAF A:JA9201 4.5 25.2 0.5
N A:LEU17 4.6 15.0 1.0
CA A:ALA108 4.6 18.4 1.0
O A:LYS15 4.7 18.9 1.0
CAC A:JA9201 4.7 26.0 0.5
CD1 A:LEU110 4.9 17.9 1.0
CAE A:JA9201 5.0 27.6 0.5

Chlorine binding site 2 out of 6 in 7eri

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Chlorine binding site 2 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:32.0
occ:0.50
 CLR A:JA9201 0.0 32.0 0.5
CAF A:JA9201 1.7 25.2 0.5
CAE A:JA9201 2.7 27.6 0.5
CAD A:JA9201 2.8 26.9 0.5
CLU A:JA9201 3.3 29.7 0.5
CB A:SER117 3.3 18.8 1.0
OG A:SER117 3.6 24.5 1.0
CD2 A:LEU110 3.6 21.2 1.0
CAC A:JA9201 4.0 26.0 0.5
CAB A:JA9201 4.0 29.0 0.5
CB A:LEU110 4.0 15.5 1.0
CG A:LEU110 4.5 17.2 1.0
CAA A:JA9201 4.5 29.9 0.5
CA A:SER117 4.8 15.5 1.0

Chlorine binding site 3 out of 6 in 7eri

Go back to Chlorine Binding Sites List in 7eri
Chlorine binding site 3 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:29.7
occ:0.50
 CLU A:JA9201 0.0 29.7 0.5
CAD A:JA9201 1.8 26.9 0.5
CAF A:JA9201 2.8 25.2 0.5
CAB A:JA9201 2.8 29.0 0.5
OAG A:JA9201 3.0 31.0 0.5
CLR A:JA9201 3.3 32.0 0.5
CLQ A:JA9201 3.8 32.1 0.5
O A:SER117 3.8 16.1 1.0
O A:ALA108 3.9 22.1 1.0
CG2 A:THR119 4.0 20.8 1.0
C A:SER117 4.1 17.8 1.0
CB A:SER117 4.1 18.8 1.0
N A:THR119 4.1 17.7 1.0
CAE A:JA9201 4.1 27.6 0.5
CAA A:JA9201 4.1 29.9 0.5
CA A:THR118 4.2 17.6 1.0
CAH A:JA9201 4.2 30.1 0.5
C A:ALA108 4.2 21.0 1.0
N A:LEU110 4.2 15.8 1.0
C A:THR118 4.3 18.2 1.0
N A:THR118 4.3 18.2 1.0
CB A:LEU110 4.3 15.5 1.0
CA A:ALA109 4.4 18.0 1.0
CB A:THR119 4.4 17.6 1.0
C A:ALA109 4.5 20.6 1.0
N A:ALA109 4.5 16.7 1.0
CB A:ALA108 4.5 22.2 1.0
CAI A:JA9201 4.5 31.5 0.5
CAC A:JA9201 4.6 26.0 0.5
CA A:SER117 4.8 15.5 1.0
CA A:THR119 4.9 18.8 1.0
O A:THR118 4.9 20.9 1.0
CA A:LEU110 4.9 15.9 1.0

Chlorine binding site 4 out of 6 in 7eri

Go back to Chlorine Binding Sites List in 7eri
Chlorine binding site 4 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:37.5
occ:0.50
 CLQ B:JA9201 0.0 37.5 0.5
CAI B:JA9201 1.6 34.8 0.5
CAK B:JA9201 2.6 35.7 0.5
CAH B:JA9201 2.7 32.5 0.5
OAG B:JA9201 2.9 33.8 0.5
CB B:ALA108 3.1 20.3 1.0
CAM B:JA9201 3.8 35.8 0.5
CG2 B:THR119 3.9 22.9 1.0
CAJ B:JA9201 3.9 33.6 0.5
CAB B:JA9201 4.0 31.9 0.5
CG2 B:VAL121 4.3 28.2 1.0
CAL B:JA9201 4.4 35.1 0.5
CA B:ALA108 4.6 15.3 1.0
CAA B:JA9201 4.7 28.8 0.5
CAD B:JA9201 5.0 29.3 0.5
N B:ALA108 5.0 17.1 1.0
NAN B:JA9201 5.0 37.0 0.5

Chlorine binding site 5 out of 6 in 7eri

Go back to Chlorine Binding Sites List in 7eri
Chlorine binding site 5 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:32.5
occ:0.50
 CLR B:JA9201 0.0 32.5 0.5
CAF B:JA9201 1.8 27.8 0.5
CAE B:JA9201 2.7 28.3 0.5
CAD B:JA9201 2.8 29.3 0.5
CLU B:JA9201 3.2 31.6 0.5
CB B:SER117 3.4 19.6 1.0
OG B:SER117 3.8 23.4 1.0
CAC B:JA9201 4.0 26.9 0.5
CAB B:JA9201 4.1 31.9 0.5
CD2 B:LEU110 4.2 22.2 1.0
CAA B:JA9201 4.6 28.8 0.5
CB B:LEU110 4.7 19.2 1.0
CA B:SER117 4.8 16.2 1.0

Chlorine binding site 6 out of 6 in 7eri

Go back to Chlorine Binding Sites List in 7eri
Chlorine binding site 6 out of 6 in the Crystal Structure of V30M-Ttr in Complex with Triclabendazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of V30M-Ttr in Complex with Triclabendazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:31.6
occ:0.50
 CLU B:JA9201 0.0 31.6 0.5
CAD B:JA9201 1.8 29.3 0.5
CAF B:JA9201 2.7 27.8 0.5
CAB B:JA9201 2.8 31.9 0.5
OAG B:JA9201 3.0 33.8 0.5
CLR B:JA9201 3.2 32.5 0.5
O B:SER117 4.0 17.4 1.0
CG2 B:THR119 4.0 22.9 1.0
CAE B:JA9201 4.0 28.3 0.5
CAA B:JA9201 4.1 28.8 0.5
CB B:LEU110 4.1 19.2 1.0
O B:ALA108 4.1 20.4 1.0
N B:THR119 4.3 15.9 1.0
CB B:ALA108 4.3 20.3 1.0
N B:LEU110 4.3 15.6 1.0
CAH B:JA9201 4.3 32.5 0.5
C B:SER117 4.3 16.8 1.0
CB B:SER117 4.4 19.6 1.0
C B:ALA108 4.4 16.1 1.0
CA B:THR118 4.5 16.1 1.0
C B:THR118 4.5 17.0 1.0
CB B:THR119 4.5 20.9 1.0
CAC B:JA9201 4.6 26.9 0.5
N B:THR118 4.6 16.6 1.0
C B:ALA109 4.7 18.4 1.0
N B:ALA109 4.7 19.8 1.0
CA B:ALA109 4.8 17.3 1.0
CA B:LEU110 4.8 14.4 1.0

Reference:

T.Yokoyama, M.Kashihara, M.Mizuguchi. Repositioning of the Anthelmintic Drugs Bithionol and Triclabendazole As Transthyretin Amyloidogenesis Inhibitors. J.Med.Chem. V. 64 14344 2021.
ISSN: ISSN 0022-2623
PubMed: 34547896
DOI: 10.1021/ACS.JMEDCHEM.1C00823
Page generated: Mon Jul 29 20:34:58 2024

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