Iodine in PDB 6dfn: Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA

The structure of Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA, PDB code: 6dfn was solved by J.R.Kiefer, M.Vinogradova, J.Liang, B.Zhang, D.F.Ortwine, K.W.Nettles, J.C.Nwachukwu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.089, 59.134, 94.180, 86.05, 74.92, 63.34
R / Rfree (%)	24.8 / 26.5

The structure of Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Nickel	(Ni)	1 atom

The binding sites of Iodine atom in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA (pdb code 6dfn). 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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA, PDB code: 6dfn:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:66.2 occ:1.00 I19 A:G9J601 0.0 66.2 1.0 C16 A:G9J601 2.1 56.1 1.0 C15 A:G9J601 3.0 53.4 1.0 C17 A:G9J601 3.0 55.5 1.0 O A:VAL533 3.1 71.3 1.0 C A:VAL533 3.9 73.2 1.0 CB A:VAL533 4.2 75.1 1.0 CH2 A:TRP383 4.2 48.2 1.0 C18 A:G9J601 4.3 54.5 1.0 C14 A:G9J601 4.3 55.5 1.0 OD1 A:ASP351 4.3 61.3 1.0 CG2 A:THR347 4.4 54.5 1.0 N A:VAL534 4.5 72.2 1.0 CA A:VAL534 4.5 69.9 1.0 CZ3 A:TRP383 4.6 48.4 1.0 CD1 A:LEU525 4.6 62.7 1.0 CB A:ALA350 4.6 49.0 1.0 CA A:VAL533 4.7 75.1 1.0 CD2 A:LEU525 4.8 65.6 1.0 CD A:PRO535 4.8 66.8 1.0 C13 A:G9J601 4.8 53.6 1.0 OG1 A:THR347 4.9 55.0 1.0 CG1 A:VAL534 5.0 70.2 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA within 5.0Å range: probe atom residue distance (Å) B Occ B:I602 b:82.5 occ:0.50 I19 B:G9J602 0.0 82.5 0.5 C30 B:G91601 0.9 60.5 0.5 O29 B:G91601 1.1 58.8 0.5 C3 B:G91601 1.8 55.3 0.5 C16 B:G9J602 2.1 73.3 0.5 C31 B:G91601 2.2 60.7 0.5 C4 B:G91601 2.2 53.7 0.5 N32 B:G91601 2.7 61.3 0.5 C17 B:G9J602 3.0 71.6 0.5 C2 B:G91601 3.0 53.4 0.5 C15 B:G9J602 3.0 71.6 0.5 C5 B:G91601 3.5 53.1 0.5 C33 B:G91601 3.6 61.2 0.5 C1 B:G91601 4.1 52.4 0.5 C35 B:G91601 4.1 61.3 0.5 OD1 B:ASP351 4.3 65.2 1.0 CG2 B:THR347 4.3 66.5 1.0 C6 B:G91601 4.3 52.4 0.5 C18 B:G9J602 4.3 69.8 0.5 C14 B:G9J602 4.3 69.4 0.5 CH2 B:TRP383 4.5 49.1 1.0 CB B:ALA350 4.5 51.0 1.0 CD1 B:LEU525 4.7 64.5 1.0 OG1 B:THR347 4.7 65.3 1.0 CZ3 B:TRP383 4.7 47.9 1.0 C34 B:G91601 4.8 60.9 0.5 CD2 B:LEU525 4.9 68.2 1.0 C13 B:G9J602 4.9 68.4 0.5 CB B:THR347 4.9 66.4 1.0 CA B:THR347 4.9 63.6 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA within 5.0Å range: probe atom residue distance (Å) B Occ C:I601 b:67.0 occ:1.00 I19 C:G9J601 0.0 67.0 1.0 C16 C:G9J601 2.1 59.3 1.0 C17 C:G9J601 3.0 55.9 1.0 C15 C:G9J601 3.0 55.6 1.0 O C:VAL533 3.2 77.0 1.0 C C:VAL533 4.0 78.8 1.0 CH2 C:TRP383 4.2 50.3 1.0 C18 C:G9J601 4.3 58.1 1.0 C14 C:G9J601 4.3 55.8 1.0 CB C:VAL533 4.3 80.5 1.0 OD1 C:ASP351 4.4 61.2 1.0 CG2 C:THR347 4.4 53.7 1.0 CZ3 C:TRP383 4.5 49.9 1.0 CB C:ALA350 4.6 48.8 1.0 CD1 C:LEU525 4.6 59.3 1.0 CA C:VAL534 4.6 76.7 1.0 N C:VAL534 4.6 77.7 1.0 OG1 C:THR347 4.8 53.6 1.0 CD C:PRO535 4.8 73.7 1.0 C13 C:G9J601 4.9 56.4 1.0 CD2 C:LEU525 4.9 60.8 1.0 CA C:VAL533 4.9 80.0 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AA within 5.0Å range: probe atom residue distance (Å) B Occ D:I601 b:71.1 occ:0.50 I19 D:G9J601 0.0 71.1 0.5 C30 D:G91602 1.0 65.5 0.5 O29 D:G91602 1.1 62.4 0.5 C31 D:G91602 1.8 66.7 0.5 C16 D:G9J601 2.1 62.5 0.5 C3 D:G91602 2.1 60.8 0.5 C4 D:G91602 2.9 60.9 0.5 N32 D:G91602 2.9 67.8 0.5 C17 D:G9J601 3.0 60.4 0.5 C15 D:G9J601 3.0 61.5 0.5 C2 D:G91602 3.2 60.2 0.5 C35 D:G91602 3.6 68.6 0.5 CH2 D:TRP383 4.1 47.7 1.0 C5 D:G91602 4.2 60.5 0.5 C33 D:G91602 4.2 69.3 0.5 C18 D:G9J601 4.3 58.5 0.5 C14 D:G9J601 4.4 58.7 0.5 CD1 D:LEU525 4.4 60.6 1.0 C1 D:G91602 4.4 60.0 0.5 CZ3 D:TRP383 4.5 46.9 1.0 OD1 D:ASP351 4.5 68.0 1.0 CA D:VAL534 4.6 0.6 1.0 CD2 D:LEU525 4.7 64.2 1.0 CD D:PRO535 4.7 0.3 1.0 CG2 D:THR347 4.8 61.3 1.0 N D:VAL534 4.8 0.5 1.0 C6 D:G91602 4.8 60.2 0.5 C13 D:G9J601 4.9 58.3 0.5 C34 D:G91602 4.9 69.4 0.5 CB D:ALA350 4.9 51.0 1.0 CG2 D:VAL534 5.0 0.8 1.0

B.Zhang, J.R.Kiefer, R.A.Blake, J.H.Chang, S.Hartman, E.R.Ingalla, T.Kleinheinz, V.Mody, M.Nannini, D.F.Ortwine, Y.Ran, A.Sambrone, D.Sampath, M.Vinogradova, Y.Zhong, J.C.Nwachukwu, K.W.Nettles, T.Lai, J.Liao, X.Zheng, H.Chen, X.Wang, J.Liang. Unexpected Equivalent Potency of A Constrained Chromene Enantiomeric Pair Rationalized By Co-Crystal Structures in Complex with Estrogen Receptor Alpha. Bioorg. Med. Chem. Lett. V. 29 905 2019.
ISSN: ESSN 1464-3405
PubMed: 30732944
DOI: 10.1016/J.BMCL.2019.01.036