Iodine in PDB 8wgs: Crystal Structure of V30M-Ttr in Complex with Compound 4

The structure of Crystal Structure of V30M-Ttr in Complex with Compound 4, PDB code: 8wgs was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.329, 85.949, 63.863, 90, 90, 90
R / Rfree (%)	18.7 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of V30M-Ttr in Complex with Compound 4 (pdb code 8wgs). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of V30M-Ttr in Complex with Compound 4, PDB code: 8wgs:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:33.4 occ:0.15 IAN A:WGH201 0.0 33.4 0.1 IAN A:WGH201 1.7 45.3 0.3 CAJ A:WGH201 2.2 34.1 0.1 OAO A:WGH201 2.7 36.6 0.3 CAJ A:WGH201 2.9 34.1 0.3 CAL A:WGH201 3.1 34.1 0.1 CAH A:WGH201 3.2 33.1 0.1 CAL A:WGH201 3.2 33.8 0.3 OAO A:WGH201 3.2 35.5 0.1 CD A:LYS15 3.8 35.9 1.0 CAH A:WGH201 4.1 31.5 0.3 CG2 A:THR106 4.2 27.4 1.0 CE A:MET13 4.5 38.9 1.0 CAK A:WGH201 4.5 33.6 0.1 CAG A:WGH201 4.5 31.5 0.1 CB A:LYS15 4.6 24.3 1.0 CAK A:WGH201 4.6 35.7 0.3 CG A:LYS15 4.7 27.3 1.0 NZ A:LYS15 4.8 47.3 1.0 CE A:LYS15 4.9 36.0 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:45.3 occ:0.35 IAN A:WGH201 0.0 45.3 0.3 CAJ A:WGH201 1.6 34.1 0.1 IAN A:WGH201 1.7 33.4 0.1 CAH A:WGH201 1.8 33.1 0.1 CAJ A:WGH201 2.1 34.1 0.3 CAL A:WGH201 3.0 34.1 0.1 CAH A:WGH201 3.0 31.5 0.3 CAL A:WGH201 3.2 33.8 0.3 CAG A:WGH201 3.2 31.5 0.1 OAO A:WGH201 3.3 36.6 0.3 OAO A:WGH201 3.7 35.5 0.1 CAK A:WGH201 4.0 33.6 0.1 CAI A:WGH201 4.1 31.5 0.1 OAM A:WGH201 4.1 30.6 0.1 CAF A:WGH201 4.1 30.5 0.1 CAG A:WGH201 4.4 31.1 0.3 CB A:ALA108 4.4 28.1 1.0 CG2 A:THR106 4.5 27.4 1.0 CAK A:WGH201 4.5 35.7 0.3 CD A:LYS15 4.8 35.9 1.0 CG2 A:VAL121 4.9 33.3 1.0 CAI A:WGH201 4.9 33.8 0.3

Iodine binding site 3 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:39.8 occ:0.15 IAP A:WGH201 0.0 39.8 0.1 CAK A:WGH201 1.6 35.7 0.3 CAI A:WGH201 1.6 33.8 0.3 IAP A:WGH201 1.8 44.0 0.3 CAK A:WGH201 2.1 33.6 0.1 CAL A:WGH201 3.0 33.8 0.3 CAG A:WGH201 3.0 31.1 0.3 CAI A:WGH201 3.0 31.5 0.1 CAL A:WGH201 3.1 34.1 0.1 OAO A:WGH201 3.2 35.5 0.1 CD1 A:LEU17 3.7 31.5 1.0 OAM A:WGH201 3.8 30.3 0.3 OAO A:WGH201 3.8 36.6 0.3 CAF A:WGH201 3.8 30.6 0.3 CAH A:WGH201 3.9 31.5 0.3 CAJ A:WGH201 3.9 34.1 0.3 CAG A:WGH201 4.3 31.5 0.1 CAJ A:WGH201 4.4 34.1 0.1 NZ A:LYS15 4.7 47.3 1.0 CG A:LEU17 4.7 28.4 1.0 CE A:LYS15 4.8 36.0 1.0 CAH A:WGH201 4.9 33.1 0.1 CD2 A:LEU17 4.9 28.0 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:44.0 occ:0.35 IAP A:WGH201 0.0 44.0 0.3 IAP A:WGH201 1.8 39.8 0.1 CAK A:WGH201 2.2 35.7 0.3 OAO A:WGH201 2.8 35.5 0.1 CAI A:WGH201 3.1 33.8 0.3 CAK A:WGH201 3.1 33.6 0.1 CAL A:WGH201 3.2 33.8 0.3 OAO A:WGH201 3.3 36.6 0.3 CAL A:WGH201 3.4 34.1 0.1 NZ A:LYS15 3.4 47.3 1.0 CE A:LYS15 4.0 36.0 1.0 CAI A:WGH201 4.4 31.5 0.1 CAG A:WGH201 4.4 31.1 0.3 CAJ A:WGH201 4.5 34.1 0.3 CD1 A:LEU17 4.7 31.5 1.0 CAJ A:WGH201 4.8 34.1 0.1 CD A:LYS15 4.9 35.9 1.0 CAH A:WGH201 5.0 31.5 0.3

Iodine binding site 5 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:27.1 occ:0.15 IAW A:WGH201 0.0 27.1 0.1 CAQ A:WGH201 2.1 27.7 0.1 CAR A:WGH201 3.0 29.5 0.1 IAW A:WGH201 3.0 36.4 0.3 CAD A:WGH201 3.0 29.7 0.1 CAF A:WGH201 3.4 30.5 0.1 CAC A:WGH201 3.5 29.9 0.1 OAM A:WGH201 3.7 30.6 0.1 CAG A:WGH201 3.8 31.5 0.1 CAI A:WGH201 4.0 31.5 0.1 CAF A:WGH201 4.0 30.6 0.3 CAQ A:WGH201 4.1 28.9 0.3 OAM A:WGH201 4.2 30.3 0.3 CAG A:WGH201 4.2 31.1 0.3 CAH A:WGH201 4.2 31.5 0.3 CAE A:WGH201 4.3 29.5 0.1 CAT A:WGH201 4.3 26.0 0.1 CAD A:WGH201 4.5 29.9 0.3 CAC A:WGH201 4.5 30.4 0.3 CAH A:WGH201 4.7 33.1 0.1 CAS A:WGH201 4.8 28.5 0.1 CAA A:WGH201 4.8 29.9 0.1 CAR A:WGH201 4.9 28.2 0.3 CAK A:WGH201 5.0 33.6 0.1

Iodine binding site 6 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:36.4 occ:0.35 IAW A:WGH201 0.0 36.4 0.3 CAR A:WGH201 0.8 29.5 0.1 CAQ A:WGH201 1.0 27.7 0.1 CAT A:WGH201 1.4 26.0 0.1 CAD A:WGH201 1.6 29.7 0.1 CAS A:WGH201 1.8 28.5 0.1 CAE A:WGH201 1.9 29.5 0.1 CAQ A:WGH201 2.1 28.9 0.3 CAC A:WGH201 2.9 29.9 0.1 CAR A:WGH201 3.0 28.2 0.3 OAM A:WGH201 3.0 30.3 0.3 IAW A:WGH201 3.0 27.1 0.1 CAD A:WGH201 3.1 29.9 0.3 OAB A:WGH201 3.1 29.9 0.1 CAF A:WGH201 3.4 30.6 0.3 CAA A:WGH201 3.6 29.9 0.1 CAC A:WGH201 3.6 30.4 0.3 CAF A:WGH201 3.9 30.5 0.1 CAT A:WGH201 4.3 30.8 0.3 CAE A:WGH201 4.3 30.1 0.3 CAG A:WGH201 4.5 31.1 0.3 OAM A:WGH201 4.5 30.6 0.1 CAI A:WGH201 4.6 31.5 0.1 CAG A:WGH201 4.7 31.5 0.1 CAS A:WGH201 4.8 26.3 0.3 CAA A:WGH201 4.9 30.2 0.3

Iodine binding site 7 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:30.8 occ:0.15 IAN B:WGH201 0.0 30.8 0.1 IAN B:WGH201 1.1 47.3 0.3 CAJ B:WGH201 2.2 37.5 0.1 CAJ B:WGH201 2.5 37.2 0.3 CAH B:WGH201 3.1 35.5 0.3 CAL B:WGH201 3.1 36.2 0.1 CAH B:WGH201 3.2 34.8 0.1 OAO B:WGH201 3.2 37.9 0.1 CAL B:WGH201 3.6 35.9 0.3 CG2 B:VAL121 3.8 33.8 1.0 OAO B:WGH201 3.9 38.6 0.3 CG2 B:THR106 4.1 31.7 1.0 CB B:VAL121 4.4 30.8 1.0 CAG B:WGH201 4.4 32.8 0.3 CAK B:WGH201 4.5 35.4 0.1 CAG B:WGH201 4.5 32.9 0.1 CB B:THR106 4.5 32.3 1.0 CG1 B:VAL121 4.6 33.1 1.0 CAK B:WGH201 4.8 35.6 0.3 OG1 B:THR106 4.8 36.0 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:47.3 occ:0.35 IAN B:WGH201 0.0 47.3 0.3 IAN B:WGH201 1.1 30.8 0.1 CAJ B:WGH201 2.1 37.2 0.3 CAJ B:WGH201 2.1 37.5 0.1 OAO B:WGH201 2.6 37.9 0.1 CAL B:WGH201 2.7 36.2 0.1 CAL B:WGH201 3.1 35.9 0.3 CAH B:WGH201 3.1 35.5 0.3 OAO B:WGH201 3.2 38.6 0.3 CAH B:WGH201 3.3 34.8 0.1 CG2 B:THR106 4.0 31.7 1.0 CAK B:WGH201 4.1 35.4 0.1 CAK B:WGH201 4.4 35.6 0.3 CAG B:WGH201 4.4 32.8 0.3 CD B:LYS15 4.5 35.8 1.0 CAG B:WGH201 4.5 32.9 0.1 CG2 B:VAL121 4.7 33.8 1.0 CB B:THR106 4.7 32.3 1.0 CE B:MET13 4.8 43.7 1.0 CAI B:WGH201 4.8 33.2 0.1 CAI B:WGH201 4.9 33.1 0.3 OG1 B:THR106 4.9 36.0 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:41.6 occ:0.15 IAP B:WGH201 0.0 41.6 0.1 IAP B:WGH201 0.8 48.9 0.3 CAK B:WGH201 1.8 35.6 0.3 CAK B:WGH201 2.1 35.4 0.1 CAL B:WGH201 2.6 35.9 0.3 OAO B:WGH201 2.6 38.6 0.3 CAI B:WGH201 3.0 33.1 0.3 CAI B:WGH201 3.0 33.2 0.1 CAL B:WGH201 3.0 36.2 0.1 OAO B:WGH201 3.2 37.9 0.1 CAJ B:WGH201 3.9 37.2 0.3 CE B:LYS15 4.1 39.3 1.0 CAG B:WGH201 4.2 32.8 0.3 CAG B:WGH201 4.3 32.9 0.1 CAJ B:WGH201 4.4 37.5 0.1 CD1 B:LEU17 4.5 34.2 1.0 CAH B:WGH201 4.6 35.5 0.3 CAU B:WGH201 4.8 30.5 0.3 CAH B:WGH201 4.8 34.8 0.1 CD B:LYS15 4.8 35.8 1.0 NZ B:LYS15 4.9 48.4 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of V30M-Ttr in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of V30M-Ttr in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:48.9 occ:0.35 IAP B:WGH201 0.0 48.9 0.3 IAP B:WGH201 0.8 41.6 0.1 CAK B:WGH201 2.1 35.6 0.3 CAK B:WGH201 2.4 35.4 0.1 CAI B:WGH201 3.0 33.1 0.3 CAI B:WGH201 3.1 33.2 0.1 CAL B:WGH201 3.1 35.9 0.3 OAO B:WGH201 3.3 38.6 0.3 CAL B:WGH201 3.6 36.2 0.1 OAO B:WGH201 3.8 37.9 0.1 CD1 B:LEU17 3.9 34.2 1.0 CE B:LYS15 4.1 39.3 1.0 CAG B:WGH201 4.3 32.8 0.3 CAJ B:WGH201 4.4 37.2 0.3 CAG B:WGH201 4.4 32.9 0.1 CAJ B:WGH201 4.8 37.5 0.1 CG B:LEU17 4.9 30.2 1.0 CAH B:WGH201 4.9 35.5 0.3 CAU B:WGH201 4.9 30.5 0.3 NZ B:LYS15 5.0 48.4 1.0

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