MolNFT v1 · #62156 · protein

Glucocorticoid receptor lbd bound to GSK866

3E7C: “Glucocorticoid receptor lbd bound to GSK866”. X-ray diffraction, 1 ligand (866), 4 pockets (best druggability 0.85). MolNFT v1 #62156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3E7C
Type: protein
Length: 514 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; Nuclear receptor coactivator 2
UniProt: P04150, Q15596
Ligands: 866
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	248	65% helix, 5% strand	P04150
H	Nuclear receptor coactivator 2	protein	11	64% helix, 0% strand	Q15596
B	Glucocorticoid receptor	protein	245	64% helix, 5% strand	P04150
D	Nuclear receptor coactivator 2	protein	10	70% helix, 0% strand	Q15596

Ligands and binding sites

866 · 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.85	0.93	48	866, GOL
2	353	0.85	0.93	46	866, GOL
3	346	0.57	0.75	39	empty
4	125	0.39	0.75	20	empty

Interfaces

3 interfaces between chains.

A–B · 694 Å² buried · 2 hydrogen bonds · protein-protein
A–H · 604 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 580 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3E7C · Glucocorticoid Receptor LBD bound to GSK866 · 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 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 P04150
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 3E7C · PDBe 3E7C · UniProt P04150 · UniProt Q15596

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