MolNFT v1 · #116980 · protein

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

5DUG · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a sulfoxide-bridged oxabicyclic…”. X-ray diffraction, 1 ligand (5FV), 6 pockets (best druggability 0.85). MolNFT v1 #116980 on GenesisL1: 3D…

PDB: 5DUG
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: 5FV
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	234	71% helix, 4% strand	P03372
B	Estrogen receptor	protein	234	71% helix, 4% strand	P03372
C	Nuclear receptor coactivator 2	protein	10	60% helix, 0% strand	Q15596
D	Nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	Q15596

Ligands and binding sites

5FV · phenyl (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

6 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	246	0.85	0.96	27	5FV
2	243	0.85	0.96	29	5FV
3	67	0.59	0.89	17	empty
4	63	0.59	0.90	17	empty
5	259	0.55	0.77	34	empty

Interfaces

3 interfaces between chains.

A–B · 1609 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 512 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 494 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5DUG · 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 B against A, TM-score 0.99

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 5DUG · PDBe 5DUG · UniProt P03372 · UniProt Q15596

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