Bromine in PDB 8ii4: Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm

The structure of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm, PDB code: 8ii4 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.44 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.264, 85.656, 63.886, 90, 90, 90
R / Rfree (%)	18.3 / 19.9

The binding sites of Bromine atom in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm (pdb code 8ii4). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm, PDB code: 8ii4:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:32.6 occ:0.25 BRA A:PKQ201 0.0 32.6 0.2 CAJ A:PKQ201 1.9 30.1 0.2 CAV A:PKQ201 2.5 32.4 0.2 CAL A:PKQ201 2.9 29.6 0.2 CAH A:PKQ201 2.9 31.4 0.2 OAO A:PKQ201 3.0 31.8 0.2 OAB A:PKQ201 3.2 33.8 0.2 CAU A:PKQ201 3.8 33.2 0.2 NZ A:LYS15 3.8 48.2 1.0 CAA A:PKQ201 3.8 31.3 0.2 CAK A:PKQ201 4.2 32.1 0.2 CAE A:PKQ201 4.2 31.5 0.2 CAG A:PKQ201 4.2 29.4 0.2 CE A:LYS15 4.7 34.3 1.0 CAI A:PKQ201 4.7 30.2 0.2 CAS A:PKQ201 4.7 32.7 0.2 CAC A:PKQ201 4.9 30.8 0.2

Bromine binding site 2 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:28.9 occ:0.25 BRA A:PKQ201 0.0 28.9 0.2 CAJ A:PKQ201 1.9 27.3 0.2 CAS A:PKQ201 2.0 25.2 0.2 CAE A:PKQ201 2.7 28.6 0.2 CAH A:PKQ201 2.8 26.3 0.2 CAL A:PKQ201 2.9 29.8 0.2 OAB A:PKQ201 3.0 23.5 0.2 CAT A:PKQ201 3.0 28.0 0.2 OAO A:PKQ201 3.1 29.9 0.2 O A:SER117 3.3 24.6 1.0 OAW A:PKQ201 3.3 26.9 0.2 C A:SER117 3.5 21.4 1.0 CA A:THR118 3.7 19.6 1.0 N A:THR118 3.7 18.3 1.0 N A:THR119 3.8 17.8 1.0 CB A:SER117 3.8 24.7 1.0 C A:THR118 3.9 18.6 1.0 CAD A:PKQ201 3.9 26.9 0.2 O A:ALA108 4.0 20.4 1.0 CG2 A:THR119 4.0 24.2 1.0 N A:LEU110 4.0 15.8 1.0 CAG A:PKQ201 4.1 28.9 0.2 CAK A:PKQ201 4.2 28.7 0.2 CAR A:PKQ201 4.2 26.0 0.2 CB A:LEU110 4.2 18.7 1.0 CAA A:PKQ201 4.2 28.0 0.2 CB A:THR119 4.3 21.9 1.0 CA A:SER117 4.3 21.0 1.0 C A:ALA108 4.3 21.0 1.0 CA A:ALA109 4.4 18.0 1.0 C A:ALA109 4.5 18.9 1.0 CAQ A:PKQ201 4.5 28.6 0.2 N A:ALA109 4.6 19.4 1.0 CB A:ALA108 4.6 22.7 1.0 O A:THR118 4.6 21.7 1.0 CA A:THR119 4.6 17.2 1.0 CAI A:PKQ201 4.7 29.1 0.2 CAC A:PKQ201 4.7 28.3 0.2 CA A:LEU110 4.8 16.0 1.0

Bromine binding site 3 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:29.9 occ:0.25 BRB A:PKQ201 0.0 29.9 0.2 CAT A:PKQ201 0.8 32.3 0.2 CAR A:PKQ201 1.2 32.4 0.2 CAS A:PKQ201 1.3 32.7 0.2 CAQ A:PKQ201 1.8 32.3 0.2 CAK A:PKQ201 1.8 32.1 0.2 CAE A:PKQ201 1.9 31.5 0.2 CAD A:PKQ201 2.0 32.0 0.2 OAW A:PKQ201 2.1 30.7 0.2 CAI A:PKQ201 2.8 30.2 0.2 CAL A:PKQ201 2.8 29.6 0.2 OAO A:PKQ201 3.0 31.8 0.2 OAB A:PKQ201 3.2 33.8 0.2 CAC A:PKQ201 3.4 30.8 0.2 CAA A:PKQ201 3.8 31.3 0.2 CAG A:PKQ201 4.1 29.4 0.2 CAJ A:PKQ201 4.1 30.1 0.2 CAF A:PKQ201 4.3 30.0 0.2 CG2 A:THR106 4.4 24.9 1.0 O A:HOH358 4.6 41.6 1.0 CAH A:PKQ201 4.6 31.4 0.2 CG2 A:VAL121 4.7 28.0 1.0 OAM A:PKQ201 4.8 28.5 0.2 CD A:LYS15 4.8 32.5 1.0 CB A:ALA108 4.8 22.7 1.0 CAU A:PKQ201 4.9 27.8 0.2

Bromine binding site 4 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:42.4 occ:0.25 BRB A:PKQ201 0.0 42.4 0.2 CAR A:PKQ201 1.6 26.0 0.2 CAQ A:PKQ201 1.6 28.6 0.2 CAK A:PKQ201 1.9 28.7 0.2 CAL A:PKQ201 2.8 29.8 0.2 CAI A:PKQ201 2.9 29.1 0.2 CAT A:PKQ201 3.0 28.0 0.2 CAD A:PKQ201 3.0 26.9 0.2 OAO A:PKQ201 3.0 29.9 0.2 OAW A:PKQ201 3.8 26.9 0.2 CAE A:PKQ201 3.8 28.6 0.2 CAS A:PKQ201 3.9 25.2 0.2 OAM A:PKQ201 3.9 28.8 0.2 CAC A:PKQ201 4.0 28.3 0.2 CAJ A:PKQ201 4.2 27.3 0.2 CAG A:PKQ201 4.2 28.9 0.2 CAF A:PKQ201 4.2 28.0 0.2 CAH A:PKQ201 4.7 26.3 0.2

Bromine binding site 5 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:54.1 occ:0.25 BRA B:PKQ201 0.0 54.1 0.2 CAV B:PKQ201 1.3 38.7 0.2 CAJ B:PKQ201 1.9 38.0 0.2 CAU B:PKQ201 2.6 36.9 0.2 CAL B:PKQ201 2.8 37.4 0.2 OAB B:PKQ201 2.8 39.7 0.2 CAH B:PKQ201 2.9 37.3 0.2 CAA B:PKQ201 3.0 37.0 0.2 OAO B:PKQ201 3.0 35.9 0.2 CAE B:PKQ201 4.0 38.7 0.2 CG2 B:THR106 4.0 27.4 1.0 CAK B:PKQ201 4.1 38.7 0.2 CAC B:PKQ201 4.1 35.7 0.2 CAG B:PKQ201 4.2 36.3 0.2 CG2 B:VAL121 4.4 31.3 1.0 CAD B:PKQ201 4.6 37.7 0.2 CD B:LYS15 4.7 30.1 1.0 CAI B:PKQ201 4.7 36.0 0.2 CAS B:PKQ201 4.8 38.1 0.2 CB B:THR106 4.9 26.7 1.0

Bromine binding site 6 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:38.2 occ:0.25 BRA B:PKQ201 0.0 38.2 0.2 CAJ B:PKQ201 1.9 33.4 0.2 CAS B:PKQ201 2.0 34.8 0.2 CAE B:PKQ201 2.3 34.1 0.2 OAB B:PKQ201 2.6 35.5 0.2 CAH B:PKQ201 2.9 34.5 0.2 CAL B:PKQ201 2.9 39.0 0.2 CAT B:PKQ201 3.0 33.0 0.2 OAO B:PKQ201 3.1 35.4 0.2 CAD B:PKQ201 3.4 36.4 0.2 OAW B:PKQ201 3.6 34.1 0.2 CAA B:PKQ201 3.7 35.9 0.2 CAR B:PKQ201 3.9 35.1 0.2 CAQ B:PKQ201 4.0 33.5 0.2 CAC B:PKQ201 4.1 35.8 0.2 CAG B:PKQ201 4.2 35.8 0.2 CAK B:PKQ201 4.2 33.6 0.2 CD2 B:LEU110 4.2 25.0 1.0 CAI B:PKQ201 4.7 36.0 0.2 CAU B:PKQ201 4.8 32.7 0.2 CAV B:PKQ201 4.9 29.7 0.2

Bromine binding site 7 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:32.4 occ:0.25 BRB B:PKQ201 0.0 32.4 0.2 CAT B:PKQ201 0.8 43.2 0.2 CAR B:PKQ201 1.2 38.7 0.2 CAS B:PKQ201 1.2 38.1 0.2 CAQ B:PKQ201 1.7 37.2 0.2 CAE B:PKQ201 1.8 38.7 0.2 CAK B:PKQ201 1.8 38.7 0.2 CAD B:PKQ201 2.0 37.7 0.2 OAW B:PKQ201 2.1 29.6 0.2 CAL B:PKQ201 2.8 37.4 0.2 CAI B:PKQ201 2.8 36.0 0.2 OAO B:PKQ201 2.9 35.9 0.2 OAB B:PKQ201 3.1 39.7 0.2 CAC B:PKQ201 3.3 35.7 0.2 CAA B:PKQ201 3.8 37.0 0.2 CAJ B:PKQ201 4.1 38.0 0.2 CAG B:PKQ201 4.1 36.3 0.2 NZ B:LYS15 4.1 50.9 1.0 CD1 B:LEU17 4.3 28.7 1.0 CAF B:PKQ201 4.3 35.9 0.2 O B:HOH307 4.4 45.4 1.0 CE B:LYS15 4.4 42.9 1.0 CAH B:PKQ201 4.6 37.3 0.2 OAM B:PKQ201 4.7 30.0 0.2 CD B:LYS15 4.8 30.1 1.0 CAU B:PKQ201 4.9 32.7 0.2 CD2 B:LEU17 5.0 26.7 1.0

Bromine binding site 8 out of 8 in the Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of V30M-Ttr in Complex with 6-Hydroxy Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:42.3 occ:0.25 BRB B:PKQ201 0.0 42.3 0.2 CAQ B:PKQ201 1.7 33.5 0.2 CAK B:PKQ201 1.9 33.6 0.2 CAR B:PKQ201 2.4 35.1 0.2 OAM B:PKQ201 2.5 36.5 0.2 CAD B:PKQ201 2.7 36.4 0.2 CAL B:PKQ201 2.9 39.0 0.2 CAI B:PKQ201 2.9 36.0 0.2 OAO B:PKQ201 3.0 35.4 0.2 CAF B:PKQ201 3.3 36.5 0.2 CAC B:PKQ201 3.3 35.8 0.2 N B:LEU110 3.7 16.6 1.0 CAT B:PKQ201 3.7 33.0 0.2 O B:ALA108 3.7 21.5 1.0 O B:SER117 3.7 25.6 1.0 C B:ALA108 3.7 20.9 1.0 CAE B:PKQ201 3.8 34.1 0.2 CB B:ALA108 3.8 22.6 1.0 N B:ALA109 3.9 17.9 1.0 C B:ALA109 3.9 21.2 1.0 CA B:ALA109 3.9 20.0 1.0 CB B:LEU110 4.0 19.8 1.0 CG2 B:THR119 4.1 22.6 1.0 N B:THR119 4.2 18.6 1.0 CAJ B:PKQ201 4.2 33.4 0.2 CAG B:PKQ201 4.2 35.8 0.2 CAS B:PKQ201 4.2 34.8 0.2 C B:SER117 4.2 20.0 1.0 CA B:THR118 4.3 19.2 1.0 CA B:LEU110 4.4 17.8 1.0 CA B:ALA108 4.4 19.8 1.0 C B:THR118 4.5 20.9 1.0 N B:THR118 4.5 18.2 1.0 CAA B:PKQ201 4.5 35.9 0.2 CAG B:PKQ201 4.6 36.3 0.2 CAH B:PKQ201 4.7 34.5 0.2 CB B:THR119 4.7 21.9 1.0 O B:ALA109 4.7 21.6 1.0 OAW B:PKQ201 4.7 34.1 0.2 CB B:SER117 4.7 30.1 1.0 OAB B:PKQ201 4.8 35.5 0.2

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