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Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4,4'-{[(3S)-3- ETHYLCYCLOHEXYLIDENE]METHANEDIYL}DIPHENOL

Analyse Crystal structure of the er-alpha ligand-binding domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DY8
Type: protein
Length: 487 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor; Nuclear receptor coactivator 2
UniProt: P03372, Q15596
Ligands: 5K4
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	233	67% helix, 4% strand	P03372
B	Estrogen receptor	protein	235	69% helix, 4% strand	P03372
C	Nuclear receptor coactivator 2	protein	10	50% helix, 0% strand	Q15596
D	Nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	Q15596

Ligands and binding sites

5K4 · 4,4'-{[(3S)-3-ethylcyclohexylidene]methanediyl}diphenol · ligand · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.84	0.97	26	5K4
2	304	0.79	0.89	35	5K4
3	89	0.67	0.91	17	empty
4	92	0.64	0.90	16	empty
5	107	0.57	0.85	21	empty

Interfaces

3 interfaces between chains.

A–B · 1643 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 534 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 531 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5DY8 · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil… · the same entry in another collection · chain A against A, TM-score 1.00
P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B 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 P03372
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 5DY8 · PDBe 5DY8 · UniProt P03372 · UniProt Q15596

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