Iodine in PDB 8ii3: Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid

The structure of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid, PDB code: 8ii3 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.79 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.416, 85.578, 63.918, 90, 90, 90
R / Rfree (%)	18.8 / 21.2

The binding sites of Iodine atom in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid (pdb code 8ii3). 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 6-Hydroxy Bid, PDB code: 8ii3:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid


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 6-Hydroxy Bid within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:44.1 occ:0.50 IAN A:PKK201 0.0 44.1 0.5 CAJ A:PKK201 2.2 32.4 0.5 CAH A:PKK201 3.1 33.2 0.5 CAL A:PKK201 3.2 26.9 0.5 OAO A:PKK201 3.3 36.9 0.5 NZ A:LYS15 3.5 40.2 1.0 CE A:LYS15 4.1 29.5 1.0 CAG A:PKK201 4.4 24.7 0.5 CAK A:PKK201 4.5 26.6 0.5 CAI A:PKK201 5.0 27.6 0.5

Iodine binding site 2 out of 4 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid


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 6-Hydroxy Bid within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:36.7 occ:0.50 IAP A:PKK201 0.0 36.7 0.5 CAK A:PKK201 2.1 26.6 0.5 CAI A:PKK201 3.0 27.6 0.5 CAL A:PKK201 3.1 26.9 0.5 OAO A:PKK201 3.3 36.9 0.5 CG2 A:THR106 4.2 23.9 1.0 CAG A:PKK201 4.4 24.7 0.5 CAJ A:PKK201 4.4 32.4 0.5 O A:HOH343 4.5 40.9 1.0 CG2 A:VAL121 4.5 24.0 1.0 CD A:LYS15 4.7 25.8 1.0 CB A:ALA108 4.8 19.5 1.0 CAU A:PKK201 4.9 20.4 0.5 CAH A:PKK201 4.9 33.2 0.5

Iodine binding site 3 out of 4 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid


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 6-Hydroxy Bid within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:37.7 occ:0.50 IAN B:PKK201 0.0 37.7 0.5 CAJ B:PKK201 2.2 33.8 0.5 CAH B:PKK201 3.1 25.3 0.5 CAL B:PKK201 3.2 28.1 0.5 OAO B:PKK201 3.3 32.3 0.5 CG2 B:THR106 4.0 24.8 1.0 CAG B:PKK201 4.5 25.6 0.5 CB B:THR106 4.5 22.2 1.0 CAK B:PKK201 4.5 28.1 0.5 OG1 B:THR106 4.6 26.6 1.0 CG2 B:VAL121 4.6 27.2 1.0 CE B:MET13 4.8 28.5 1.0 CB B:VAL121 4.9 23.8 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bid


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 6-Hydroxy Bid within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:37.2 occ:0.50 IAP B:PKK201 0.0 37.2 0.5 CAK B:PKK201 2.1 28.1 0.5 CAI B:PKK201 3.0 24.6 0.5 CAL B:PKK201 3.2 28.1 0.5 OAO B:PKK201 3.4 32.3 0.5 NZ B:LYS15 3.9 42.1 1.0 CE B:LYS15 4.1 28.1 1.0 CAG B:PKK201 4.4 25.6 0.5 CD1 B:LEU17 4.4 24.9 1.0 CAJ B:PKK201 4.5 33.8 0.5 CAU B:PKK201 4.8 20.5 0.5 CAH B:PKK201 4.9 25.3 0.5 CD B:LYS15 4.9 26.9 1.0

M.Mizuguchi, T.Yokoyama, T.Okada, Y.Nakagawa, K.Fujii, Y.Nabeshima, N.Toyooka. Benziodarone and 6-Hydroxybenziodarone Are Potent and Selective Inhibitors of Transthyretin Amyloidogenesis. Bioorg.Med.Chem. V. 90 17370 2023.
ISSN: ESSN 1464-3391
PubMed: 37311373
DOI: 10.1016/J.BMC.2023.117370