MolNFT v1 · #146361 · protein

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

6DF6: “Crystal structure of estrogen receptor alpha in complex with receptor degrader 16AB”. X-ray diffraction, 1 ligand (G8Y), 15 pockets (best druggability 0.79). MolNFT v1 #146361 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6DF6
Type: protein
Length: 919 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor
UniProt: P03372
Ligands: G8Y
Pockets: 15 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	235	70% helix, 4% strand	P03372
B	Estrogen receptor	protein	220	71% helix, 4% strand	P03372
C	Estrogen receptor	protein	233	70% helix, 4% strand	P03372
D	Estrogen receptor	protein	231	70% helix, 4% strand	P03372

Ligands and binding sites

G8Y · (8R)-8-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-1,8-dihydro-2H-[1]benzopyrano[4,3-d][1]benzoxepine-5,11-diol · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	335	0.79	0.88	28	G8Y
2	276	0.79	0.90	32	G8Y
3	288	0.78	0.89	29	G8Y
4	255	0.76	0.89	29	G8Y
5	99	0.65	0.90	20	empty

Interfaces

3 interfaces between chains.

C–D · 1587 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1460 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 307 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6DF6 · Crystal structure of estrogen receptor alpha in complex with receptor degrader 16ab · the same entry in another collection · chain D against D, 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 0.94

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
Elsewhere: RCSB PDB 6DF6 · PDBe 6DF6 · UniProt P03372

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