MolNFT v1 · #160273 · protein

Crystal structure of gdc-0927 bound to estrogen receptor alpha

6PFM: “Crystal structure of gdc-0927 bound to estrogen receptor alpha”. X-ray diffraction, 1 ligand (OGJ), 9 pockets (best druggability 0.78). MolNFT v1 #160273 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PFM
Type: protein
Length: 459 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Estrogen receptor
UniProt: P03372
Ligands: OGJ
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Estrogen receptor	protein	235	69% helix, 4% strand	P03372
A	Estrogen receptor	protein	224	70% helix, 4% strand	P03372

Ligands and binding sites

OGJ · (2S)-2-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-3-(3-hydroxyphenyl)-4-methyl-2H-1-benzopyran-6-ol · ligand · 2 copies · chains D, A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	209	0.78	0.92	23	OGJ
2	225	0.77	0.90	26	OGJ
3	97	0.66	0.90	19	empty
4	84	0.61	0.89	18	empty
5	123	0.48	0.79	21	empty

Interfaces

1 interface between chains.

D–A · 1483 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6PFM · Crystal structure of GDC-0927 bound to estrogen receptor alpha · 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 A against A, TM-score 0.97

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 6PFM · PDBe 6PFM · UniProt P03372

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