MolNFT v1 · #117209 · protein

Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative dimethyl {(1S)-3-[BIS(4- HYDROXYPHENYL)METHYLIDENE]CYCLOHEXYL}PROPANEDIOATE

5E1C · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative dimethyl…”. X-ray diffraction, 1 ligand (5K8), 6 pockets (best druggability 0.83). MolNFT v1 #117209 on GenesisL1…

PDB: 5E1C
Type: protein
Length: 500 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: 5K8
Pockets: 6 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Estrogen receptor	protein	237	73% helix, 3% strand	P03372
B	Estrogen receptor	protein	241	65% helix, 4% strand	P03372
C	Nuclear receptor coactivator 2	protein	12	58% helix, 0% strand	Q15596
D	Nuclear receptor coactivator 2	protein	10	50% helix, 0% strand	Q15596

Ligands and binding sites

5K8 · dimethyl {(1S)-3-[bis(4-hydroxyphenyl)methylidene]cyclohexyl}propanedioate · 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	282	0.83	0.93	28	5K8
2	297	0.82	0.92	31	5K8
3	479	0.68	0.79	55	empty
4	82	0.67	0.92	18	empty
5	89	0.64	0.90	20	empty

Interfaces

3 interfaces between chains.

A–B · 1628 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 606 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 537 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5E1C · 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 B 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 5E1C · PDBe 5E1C · UniProt P03372 · UniProt Q15596

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