MolNFT v1 · #140235 · protein

A moderator XD22 binding to bile acid receptor

5Y49: “A moderator XD22 binding to bile acid receptor”. X-ray diffraction, 1 ligand (XD5), 7 pockets (best druggability 0.82). MolNFT v1 #140235 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Y49
Type: protein
Length: 472 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; Peptide from nuclear receptor coactivator 2
UniProt: Q96RI1, Q15596
Ligands: XD5
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bile acid receptor	protein	224	74% helix, 0% strand	Q96RI1
B	Bile acid receptor	protein	227	75% helix, 0% strand	Q96RI1
D	Peptide from nuclear receptor coactivator 2	protein	11	73% helix, 0% strand	Q15596
E	Peptide from nuclear receptor coactivator 2	protein	10	70% helix, 0% strand	Q15596

Ligands and binding sites

XD5 · [(1R,2S,4S)-2-bicyclo[2.2.1]heptanyl] 4-azanylbenzoate · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	146	0.82	0.98	24	XD5
2	131	0.81	0.98	24	XD5
3	53	0.56	0.90	13	empty
4	103	0.56	0.84	28	empty
5	154	0.54	0.80	26	empty

Interfaces

3 interfaces between chains.

A–D · 593 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 555 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 319 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5Y49 · A moderator XD22 binding to bile acid receptor · 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 Q15596
Elsewhere: RCSB PDB 5Y49 · PDBe 5Y49 · UniProt Q96RI1 · UniProt Q15596

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