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Iodine in PDB 8wgt: Crystal Structure of V30M-Ttr in Complex with Compound 7

Protein crystallography data

The structure of Crystal Structure of V30M-Ttr in Complex with Compound 7, PDB code: 8wgt was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.54 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.536, 85.273, 63.79, 90, 90, 90
R / Rfree (%) 20.3 / 23.1

Other elements in 8wgt:

The structure of Crystal Structure of V30M-Ttr in Complex with Compound 7 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of V30M-Ttr in Complex with Compound 7 (pdb code 8wgt). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of V30M-Ttr in Complex with Compound 7, PDB code: 8wgt:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 8wgt

Go back to Iodine Binding Sites List in 8wgt
Iodine binding site 1 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of V30M-Ttr in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:32.8
occ:0.50
IAN A:WGJ201 0.0 32.8 0.5
CAJ A:WGJ201 2.1 17.1 0.5
CAL A:WGJ201 3.1 18.9 0.5
CAH A:WGJ201 3.1 20.2 0.5
OAO A:WGJ201 3.2 20.3 0.5
NZ A:LYS15 4.0 29.0 1.0
CAK A:WGJ201 4.4 18.1 0.5
CAG A:WGJ201 4.5 16.0 0.5
CE A:LYS15 4.5 20.0 1.0
CAI A:WGJ201 4.9 16.9 0.5

Iodine binding site 2 out of 4 in 8wgt

Go back to Iodine Binding Sites List in 8wgt
Iodine binding site 2 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of V30M-Ttr in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:21.7
occ:0.50
IAP A:WGJ201 0.0 21.7 0.5
CAK A:WGJ201 2.1 18.1 0.5
CAI A:WGJ201 3.0 16.9 0.5
CAL A:WGJ201 3.0 18.9 0.5
OAO A:WGJ201 3.1 20.3 0.5
CAG A:WGJ201 4.4 16.0 0.5
CAJ A:WGJ201 4.4 17.1 0.5
CG2 A:THR106 4.4 17.3 1.0
CG2 A:VAL121 4.5 15.9 1.0
CD A:LYS15 4.9 21.8 1.0
CAU A:WGJ201 4.9 14.3 0.5
CAH A:WGJ201 4.9 20.2 0.5

Iodine binding site 3 out of 4 in 8wgt

Go back to Iodine Binding Sites List in 8wgt
Iodine binding site 3 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of V30M-Ttr in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:25.0
occ:0.50
IAN B:WGJ201 0.0 25.0 0.5
CAJ B:WGJ201 2.1 20.0 0.5
O B:HOH352 2.8 37.3 1.0
CAL B:WGJ201 3.0 17.7 0.5
CAH B:WGJ201 3.1 18.6 0.5
OAO B:WGJ201 3.2 20.1 0.5
CG2 B:THR106 3.9 16.8 1.0
CAK B:WGJ201 4.4 18.2 0.5
CAG B:WGJ201 4.4 15.2 0.5
CB B:THR106 4.5 17.6 1.0
OG1 B:THR106 4.5 21.6 1.0
CG2 B:VAL121 4.7 19.3 1.0
CD B:LYS15 4.8 22.4 1.0
CAI B:WGJ201 4.9 16.4 0.5
CB B:VAL121 4.9 18.4 1.0

Iodine binding site 4 out of 4 in 8wgt

Go back to Iodine Binding Sites List in 8wgt
Iodine binding site 4 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of V30M-Ttr in Complex with Compound 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:20.5
occ:0.50
IAP B:WGJ201 0.0 20.5 0.5
CAK B:WGJ201 2.1 18.2 0.5
CAI B:WGJ201 3.0 16.4 0.5
CAL B:WGJ201 3.1 17.7 0.5
OAO B:WGJ201 3.2 20.1 0.5
NZ B:LYS15 4.0 29.0 1.0
CE B:LYS15 4.1 25.0 1.0
CD1 B:LEU17 4.3 17.3 1.0
CAG B:WGJ201 4.3 15.2 0.5
CAJ B:WGJ201 4.4 20.0 0.5
CD B:LYS15 4.8 22.4 1.0
CAU B:WGJ201 4.8 13.8 0.5
CAH B:WGJ201 4.9 18.6 0.5

Reference:

M.Mizuguchi, Y.Nakagawa, T.Yokoyama, T.Okada, K.Fujii, K.Takahashi, N.N.T.Luan, Y.Nabeshima, K.Kanamitsu, S.Nakagawa, S.Yamakawa, M.Ueda, Y.Ando, N.Toyooka. Development of Benziodarone Analogues with Enhanced Potency For Selective Binding to Transthyretin in Human Plasma. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38670538
DOI: 10.1021/ACS.JMEDCHEM.3C02286
Page generated: Mon Aug 12 03:12:37 2024

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