Chlorine in PDB 5l4m: Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)

The structure of Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr), PDB code: 5l4m was solved by C.Grundstrom, M.Hall, J.Zhang, A.Olofsson, P.Andersson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.28 / 1.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.543, 85.520, 64.012, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.8

The structure of Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) (pdb code 5l4m). 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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr), PDB code: 5l4m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:34.9 occ:0.50 CL6 A:SBK201 0.0 34.9 0.5 C06 A:SBK201 1.8 41.4 0.5 C01 A:SBK201 2.8 43.3 0.5 C05 A:SBK201 2.8 46.1 0.5 H011 A:SBK201 2.9 51.9 0.5 CL5 A:SBK201 3.2 50.2 0.5 HD22 A:LEU110 3.9 20.9 1.0 N04 A:SBK201 4.1 46.3 0.5 C02 A:SBK201 4.1 45.3 0.5 C03 A:SBK201 4.6 46.3 0.5 CD2 A:LEU110 4.8 17.4 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:50.2 occ:0.50 CL5 A:SBK201 0.0 50.2 0.5 C05 A:SBK201 1.7 46.1 0.5 N04 A:SBK201 2.6 46.3 0.5 C06 A:SBK201 2.7 41.4 0.5 CL6 A:SBK201 3.2 34.9 0.5 C03 A:SBK201 3.8 46.3 0.5 C01 A:SBK201 4.0 43.3 0.5 C02 A:SBK201 4.5 45.3 0.5 H102 A:SBK201 4.5 59.0 0.5 O12 A:SBK201 4.5 50.5 0.5 H011 A:SBK201 4.8 51.9 0.5 O09 A:SBK201 4.9 47.6 0.5

Chlorine binding site 3 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:45.7 occ:0.50 CL2 A:SBK201 0.0 45.7 0.5 C02 A:SBK201 1.8 45.3 0.5 C03 A:SBK201 2.8 46.3 0.5 C01 A:SBK201 2.8 43.3 0.5 HB1 A:ALA108 2.9 21.1 1.0 H011 A:SBK201 2.9 51.9 0.5 O09 A:SBK201 3.0 47.6 0.5 HD12 A:LEU17 3.0 22.1 1.0 HB2 A:LEU110 3.2 14.8 1.0 HG A:LEU17 3.3 18.0 1.0 O A:ALA109 3.3 14.4 1.0 C A:ALA109 3.5 11.6 1.0 H A:ALA109 3.5 16.2 1.0 HB2 A:LEU17 3.7 13.9 1.0 N A:ALA109 3.7 13.5 1.0 CD1 A:LEU17 3.8 18.4 1.0 CB A:ALA108 3.8 17.6 1.0 N A:LEU110 3.9 11.4 1.0 CG A:LEU17 3.9 15.0 1.0 HD11 A:LEU17 3.9 22.1 1.0 HA A:LEU110 4.0 14.0 1.0 N04 A:SBK201 4.0 46.3 0.5 CB A:LEU110 4.1 12.4 1.0 HB3 A:ALA108 4.1 21.1 1.0 C06 A:SBK201 4.1 41.4 0.5 CA A:ALA109 4.1 11.7 1.0 H A:LEU17 4.1 14.0 1.0 CA A:LEU110 4.2 11.7 1.0 C A:ALA108 4.2 14.2 1.0 HD13 A:LEU110 4.3 19.6 1.0 H A:LEU110 4.3 13.7 1.0 HA A:ALA109 4.3 14.0 1.0 CB A:LEU17 4.3 11.6 1.0 C10 A:SBK201 4.4 49.1 0.5 HB2 A:ALA108 4.4 21.1 1.0 O12 A:SBK201 4.5 50.5 0.5 CA A:ALA108 4.5 13.1 1.0 C05 A:SBK201 4.5 46.1 0.5 HB3 A:LEU110 4.5 14.8 1.0 HA A:ALA108 4.6 15.7 1.0 HD13 A:LEU17 4.6 22.1 1.0 HG2 A:LYS15 4.6 29.2 1.0 N A:LEU17 4.7 11.7 1.0 O A:LYS15 4.7 15.2 1.0 HA A:VAL16 4.7 14.4 1.0 H101 A:SBK201 4.7 59.0 0.5 C11 A:SBK201 4.8 50.7 0.5 O A:ALA108 4.9 16.2 1.0 CD1 A:LEU110 5.0 16.4 1.0 H102 A:SBK201 5.0 59.0 0.5 HD22 A:LEU110 5.0 20.9 1.0 HD12 A:LEU110 5.0 19.6 1.0 HG22 A:THR119 5.0 16.1 0.6

Chlorine binding site 4 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:33.2 occ:0.50 CL6 B:SBK201 0.0 33.2 0.5 C06 B:SBK201 1.8 40.2 0.5 C05 B:SBK201 2.8 45.7 0.5 C01 B:SBK201 2.8 43.4 0.5 H011 B:SBK201 2.9 52.0 0.5 CL5 B:SBK201 3.2 50.3 0.5 O B:HOH321 3.7 38.4 0.5 HD22 B:LEU110 3.8 20.6 1.0 N04 B:SBK201 4.0 45.7 0.5 C02 B:SBK201 4.1 45.8 0.5 C03 B:SBK201 4.5 45.6 0.5 CD2 B:LEU110 4.7 17.1 1.0 HD23 B:LEU110 4.8 20.6 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:50.3 occ:0.50 CL5 B:SBK201 0.0 50.3 0.5 C05 B:SBK201 1.7 45.7 0.5 N04 B:SBK201 2.5 45.7 0.5 C06 B:SBK201 2.7 40.2 0.5 CL6 B:SBK201 3.2 33.2 0.5 C03 B:SBK201 3.7 45.6 0.5 C01 B:SBK201 4.0 43.4 0.5 O13 B:SBK201 4.3 49.6 0.5 C02 B:SBK201 4.4 45.8 0.5 H102 B:SBK201 4.4 58.1 0.5 H011 B:SBK201 4.7 52.0 0.5 O09 B:SBK201 4.8 47.1 0.5 C10 B:SBK201 4.9 48.4 0.5 C11 B:SBK201 5.0 49.4 0.5

Chlorine binding site 6 out of 6 in the Crystal Structure of Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr)


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 Human Transthyretin in Complex with 3,5,6- Trichloro-2-Pyridinyloxyacetic Acid (Triclopyr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:47.5 occ:0.50 CL2 B:SBK201 0.0 47.5 0.5 C02 B:SBK201 1.7 45.8 0.5 C03 B:SBK201 2.7 45.6 0.5 C01 B:SBK201 2.8 43.4 0.5 HD12 B:LEU17 2.9 20.1 1.0 H011 B:SBK201 2.9 52.0 0.5 O09 B:SBK201 2.9 47.1 0.5 HB1 B:ALA108 2.9 19.0 1.0 HB2 B:LEU110 3.1 17.0 1.0 HG B:LEU17 3.2 15.8 1.0 O B:ALA109 3.2 13.5 1.0 HB2 B:LEU17 3.4 12.7 1.0 C B:ALA109 3.4 12.5 1.0 H B:ALA109 3.5 15.6 1.0 CD1 B:LEU17 3.6 16.8 1.0 N B:ALA109 3.7 13.0 1.0 N B:LEU110 3.7 11.4 1.0 CG B:LEU17 3.8 13.1 1.0 HA B:LEU110 3.8 15.1 1.0 CB B:ALA108 3.9 15.8 1.0 HD11 B:LEU17 3.9 20.1 1.0 N04 B:SBK201 3.9 45.7 0.5 CB B:LEU110 4.0 14.2 1.0 C06 B:SBK201 4.0 40.2 0.5 CB B:LEU17 4.1 10.6 1.0 CA B:LEU110 4.1 12.6 1.0 H B:LEU17 4.1 15.1 1.0 CA B:ALA109 4.1 13.0 1.0 HB3 B:ALA108 4.1 19.0 1.0 H B:LEU110 4.2 13.7 1.0 C B:ALA108 4.2 14.2 1.0 HD13 B:LEU110 4.3 18.7 1.0 HA B:ALA109 4.3 15.6 1.0 C10 B:SBK201 4.4 48.4 0.5 C05 B:SBK201 4.4 45.7 0.5 HD13 B:LEU17 4.4 20.1 1.0 HB2 B:ALA108 4.5 19.0 1.0 CA B:ALA108 4.5 14.6 1.0 HB3 B:LEU110 4.5 17.0 1.0 HA B:ALA108 4.5 17.5 1.0 N B:LEU17 4.5 12.5 1.0 HG2 B:LYS15 4.7 33.5 1.0 O13 B:SBK201 4.7 49.6 0.5 HA B:VAL16 4.7 17.0 1.0 H101 B:SBK201 4.7 58.1 0.5 O B:LYS15 4.7 16.8 1.0 HB3 B:LEU17 4.7 12.7 1.0 O B:ALA108 4.9 14.9 1.0 CD1 B:LEU110 4.9 15.6 1.0 H102 B:SBK201 4.9 58.1 0.5 C11 B:SBK201 4.9 49.4 0.5 HD12 B:LEU110 4.9 18.7 1.0 CA B:LEU17 4.9 11.7 1.0 HD22 B:LEU110 5.0 20.6 1.0

J.Zhang, A.Begum, K.Brannstrom, C.Grundstrom, I.Iakovleva, A.Olofsson, A.E.Sauer-Eriksson, P.L.Andersson. Structure-Based Virtual Screening Protocol For in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Environ. Sci. Technol. V. 50 11984 2016.
ISSN: ISSN 1520-5851
PubMed: 27668830
DOI: 10.1021/ACS.EST.6B02771