| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | kb0 | HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE | 4zi1 | 100 |
| 2 | jj3 | Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist | 2jj3 | 100 |
| 3 | 789 | Crystal structure of estrogen receptor beta complexed with 3-Bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one | 1zaf | 99.88 |
| 4 | gen | HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN | 1qkm | 99.78 |
| 5 | w14 | Fragment-Based Design of novel Estrogen Receptor Ligands | 3omp | 99.77 |
| 6 | est | Crystal Structure of ER beta bound to Estradiol | 5toa | 99.75 |
| 7 | 3as | Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand | 2qtu | 99.72 |
| 8 | fbr | Human estrogen receptor beta ligand-binding domain in complex with compound 45 | 2giu | 99.61 |
| 9 | gen | CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH GENISTEIN | 1x7j | 99.59 |
| 10 | e3o | STRUCTURE OF 17-EPIESTRIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLEX WITH LXXLL MOTIF FROM NCOA5 | 2j7y | 99.53 |
| 11 | est | Crystal structure of estrogen receptor beta ligand binding domain | 3ols | 99.52 |
| 12 | est | Estrogen Receptor in complex with proline-flanked LXXLL peptides | 4j26 | 99.51 |
| 13 | wv7 | Fragment-Based Design of novel Estrogen Receptor Ligands | 3omo | 99.46 |
| 14 | est | STRUCTURE OF ESTRADIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLEX WITH LXXLL MOTIF FROM NCOA5 | 2j7x | 99.39 |
| 15 | est | Estrogen Receptor in complex with proline-flanked LXXLL peptides | 4j24 | 99.27 |
| 16 | est | Crystal structure of phosphorylated estrogen receptor beta ligand binding domain | 3oll | 99.16 |
| 17 | dc8 | Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand | 2z4b | 98.79 |
| 18 | w23 | Fragment-Based Design of novel Estrogen Receptor Ligands | 3omq | 98.73 |
| 19 | i0g | Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia | 2i0g | 98.41 |
| 20 | etc | Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol | 1l2j | 98.31 |
| 21 | mon | Estrogen Receptor beta with Selective Triazine Modulator | 1nde | 95.04 |
| 22 | oht | A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta | 2fsz | 89.26 |
| 23 | aoe | RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PURE ANTIOESTROGEN ICI164,384 | 1hj1 | 81.95 |