SMTL ID : 6dfn.1 (1 other biounit)

Crystal structure of estrogen receptor alpha in complex with receptor degrader 16aa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x G9J: (2S)-3-(3-hydroxyphenyl)-2-(4-iodophenyl)-4-methyl-2H-1-benzopyran-6-ol(Non-covalent)

G9J.1: 16 residues within 4Å: Chain A: L.73, T.74, L.76, A.77, E.80, W.110, L.114, M.115, L.118, R.121, F.131, M.148, I.151, H.251, L.252, V.260 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.76, A:A.77, A:W.110, A:L.118, A:I.151, A:L.252 Hydrogen bonds: A:L.114, A:R.121, A:M.148 Water bridges: A:R.121 pi-Stacking: A:F.131 Halogen bonds: A:V.260 G9J.4: 15 residues within 4Å: Chain B: L.73, T.74, A.77, E.80, L.111, L.114, M.115, R.121, F.131, M.148, I.151, G.248, H.251, L.252 Ligands: G91.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.77, B:L.111, B:L.114, B:F.131, B:F.131, B:I.151, B:L.252, B:L.252 Hydrogen bonds: B:L.114, B:R.121, B:H.251 Water bridges: B:R.121

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 3 residues within 4Å: Chain A: H.228 Chain B: L.224, H.228 No protein-ligand interaction detected (PLIP)

1 x G91: (8S)-8-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-1,8-dihydro-2H-[1]benzopyrano[4,3-d][1]benzoxepine-5,11-diol(Non-covalent)

G91.3: 18 residues within 4Å: Chain B: L.73, T.74, L.76, A.77, D.78, E.80, W.110, L.111, M.115, L.118, R.121, F.131, M.148, I.151, G.248, H.251, L.252 Ligands: G9J.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.77, B:W.110, B:F.131, B:L.252 Hydrogen bonds: B:E.80, B:R.121, B:H.251 Salt bridges: B:D.78 pi-Stacking: B:F.131

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: A.49, P.51, P.52, H.83, R.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.83, B:R.90 GOL.6: 9 residues within 4Å: Chain A: S.239 Chain B: E.112, I.179, N.182, S.183, L.238, S.239, I.241, R.242 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.182, B:N.182, B:R.242, B:R.242, A:S.239, A:S.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Unexpected equivalent potency of a constrained chromene enantiomeric pair rationalized by co-crystal structures in complex with estrogen receptor alpha. Bioorg. Med. Chem. Lett. (2019)

Release Date

2019-02-20

Peptides

Estrogen receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Estrogen receptor

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