MolNFT v1 · #117083 · protein

Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 4-[(E)-(1S,5S)-BICYCLO[3.3.1]NON-9- YLIDENE(PHENYL)METHYL]PHENOL

5DXP · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative…”. X-ray diffraction, 1 ligand (5HX), 7 pockets (best druggability 0.84). MolNFT v1 #117083 on GenesisL1: 3D…

PDB: 5DXP
Type: protein
Length: 471 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: 5HX
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	222	68% helix, 3% strand	P03372
B	Estrogen receptor	protein	230	68% helix, 4% strand	P03372
C	Nuclear receptor coactivator 2	protein	10	70% helix, 0% strand	Q15596
D	Nuclear receptor coactivator 2	protein	9	56% helix, 0% strand	Q15596

Ligands and binding sites

5HX · 4-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(phenyl)methyl]phenol · ligand · 2 copies · chains A, B

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

Pockets

7 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	287	0.84	0.94	34	5HX
2	218	0.84	0.96	29	5HX
3	91	0.63	0.89	17	empty
4	84	0.63	0.90	17	empty
5	203	0.53	0.78	25	empty

Interfaces

3 interfaces between chains.

A–B · 1631 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 491 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 469 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DXP · 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 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 5DXP · PDBe 5DXP · UniProt P03372 · UniProt Q15596

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