MolNFT v1 · #141135 · protein

A ligand binding to fxr

5YXB · Bile acid receptor: “A ligand binding to fxr”. X-ray diffraction, 1 ligand (93O), 2 pockets (best druggability 0.84). MolNFT v1 #141135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YXB
Type: protein
Length: 234 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; Peptide from nuclear receptor coactivator 2
UniProt: Q96RI1, E7EWM1
Ligands: 93O
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bile acid receptor	protein	223	70% helix, 0% strand	Q96RI1
B	Peptide from nuclear receptor coactivator 2	protein	11	64% helix, 0% strand	E7EWM1

Ligands and binding sites

93O · 2-methoxyethyl (2E)-3-phenylprop-2-en-1-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	507	0.84	0.89	48	93O
2	156	0.44	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5YXB · A ligand binding to FXR · the same entry in another collection · chain A against A, TM-score 1.00

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 Q96RI1
Every structure of UniProt E7EWM1
Elsewhere: RCSB PDB 5YXB · PDBe 5YXB · UniProt Q96RI1 · UniProt E7EWM1

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