MolNFT v1 · #141137 · protein

A ligand F binding to fxr

5YXD · Bile acid receptor: “A ligand F binding to fxr”. X-ray diffraction, 1 ligand (93R), 2 pockets (best druggability 0.86). MolNFT v1 #141137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YXD
Type: protein
Length: 240 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; Peptide from nuclear receptor coactivator
UniProt: Q96RI1
Ligands: 93R
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bile acid receptor	protein	229	73% helix, 0% strand	Q96RI1
B	Peptide from nuclear receptor coactivator	protein	11	73% helix, 0% strand	—

Ligands and binding sites

93R · ethyl methyl 4-(2,3-dichlorophenyl)-2,6-dimethylpyridine-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	318	0.86	0.95	31	93R
2	150	0.41	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 578 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5YXD · A ligand F 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
Elsewhere: RCSB PDB 5YXD · PDBe 5YXD · UniProt Q96RI1

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