MolNFT v1 · #146939 · protein

Glucocorticoid receptor in complex with compound 11

6DXK: “Glucocorticoid receptor in complex with compound 11”. X-ray diffraction, 1 ligand (HJ4), 7 pockets (best druggability 0.78). MolNFT v1 #146939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DXK
Type: protein
Length: 495 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor
UniProt: P04150
Ligands: HJ4
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 62% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	247	62% helix, 9% strand	P04150
B	Glucocorticoid receptor	protein	248	62% helix, 8% strand	P04150

Ligands and binding sites

HJ4 · (8S,11R,13S,14S,17S)-11-[4-(dimethylamino)phenyl]-17-(3,3-dimethylbut-1-yn-1-yl)-17-hydroxy-13-methyl-1,2, 6,7,8,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name) · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	409	0.78	0.86	29	HJ4
2	432	0.77	0.85	29	HJ4
3	597	0.72	0.79	54	empty
4	153	0.62	0.85	24	empty
5	78	0.49	0.83	19	empty

Interfaces

1 interface between chains.

A–B · 509 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6DXK · Glucocorticoid Receptor in complex with Compound 11 · the same entry in another collection · chain A against A, TM-score 1.00
P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P04150
Elsewhere: RCSB PDB 6DXK · PDBe 6DXK · UniProt P04150

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