Research workbench

Fragment-based design of novel estrogen receptor ligands

Analyse Fragment-based design of novel estrogen receptor ligands in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OMP
Type: protein
Length: 473 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor beta; Nuclear receptor coactivator 1
UniProt: Q92731, Q15788
Ligands: W14
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor beta	protein	229	70% helix, 4% strand	Q92731
B	Estrogen receptor beta	protein	224	69% helix, 5% strand	Q92731
C, D	Nuclear receptor coactivator 1	protein	10	70% helix, 0% strand	Q15788

Ligands and binding sites

W14 · 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-7-ol · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.83	0.99	22	W14
2	136	0.82	0.98	21	W14
3	239	0.63	0.82	31	empty
4	84	0.61	0.89	18	empty
5	279	0.61	0.79	32	empty

Interfaces

3 interfaces between chains.

A–B · 1512 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 557 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 519 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3OMP · Fragment-Based Design of novel Estrogen Receptor Ligands · the same entry in another collection · chain A against A, TM-score 1.00
Q92731 · AlphaFold monomer V2.0 prediction for estrogen receptor beta (Q92731) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q92731
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 3OMP · PDBe 3OMP · UniProt Q92731 · UniProt Q15788

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