MolNFT v1 · #116978 · protein

Crystal structure of the er-alpha ligand-binding domain in complex with a para-hydroxyl-substituted, sulfoxide-bridged oxabicyclic heptene sulfonate (sobhs)-2 analog 4-hydroxyphenyl (1S,2S,4S,5S,6R, 7S)-5,6-BIS(4-hydroxy-2-methylphenyl)-7-THIABICYCLO[2.2.1]HEPTANE-2- sulfonate 7-oxide

5DUE · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a para-hydroxyl-substituted…”. X-ray diffraction, 1 ligand (5FY), 9 pockets (best druggability 0.83). MolNFT v1 #116978 on GenesisL1: 3D…

PDB: 5DUE
Type: protein
Length: 496 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: 5FY
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	235	68% helix, 3% strand	P03372
B	Estrogen receptor	protein	242	69% helix, 4% strand	P03372
C	Nuclear receptor coactivator 2	protein	10	70% helix, 0% strand	Q15596
D	Nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	Q15596

Ligands and binding sites

5FY · 4-hydroxyphenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-2-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	284	0.83	0.94	31	5FY
2	303	0.83	0.93	35	5FY
3	83	0.62	0.90	18	empty
4	73	0.60	0.89	17	empty
5	244	0.51	0.75	34	empty

Interfaces

3 interfaces between chains.

A–B · 1683 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 533 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 498 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DUE · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with a… · 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 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 P03372
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 5DUE · PDBe 5DUE · UniProt P03372 · UniProt Q15596

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