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Ligand binding to farnesoid-X-receptor

Analyse Ligand binding to farnesoid-X-receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Q1H
Type: protein
Length: 956 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; Coactivator peptide src-1 HD3
UniProt: Q96RI1, A8K1V4
Ligands: 9NP
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Bile acid receptor	protein	229	72% helix, 0% strand	Q96RI1
B	Coactivator peptide src-1 HD3	protein	11	73% helix, 0% strand	A8K1V4
C	Bile acid receptor	protein	228	74% helix, 0% strand	Q96RI1
D, H	Coactivator peptide src-1 HD3	protein	10	70% helix, 0% strand	A8K1V4
E	Bile acid receptor	protein	230	72% helix, 0% strand	Q96RI1
F	Coactivator peptide src-1 HD3	protein	9	78% helix, 0% strand	A8K1V4

Ligands and binding sites

9NP · (2S)-N,2-dicyclohexyl-2-{2-[4-(1H-tetrazol-5-yl) phenyl]-1H-benzimidazol-1-yl}acetamide · ligand · 4 copies · chains A, C, E, G

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.85	0.95	31	9NP
2	329	0.85	0.94	36	9NP
3	421	0.83	0.91	51	9NP
4	413	0.82	0.90	50	9NP
5	752	0.80	0.83	86	empty

Interfaces

9 interfaces between chains.

A–G · 1032 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 1013 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 593 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 587 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 585 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5Q1H · Ligand binding to FARNESOID-X-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 A8K1V4
Elsewhere: RCSB PDB 5Q1H · PDBe 5Q1H · UniProt Q96RI1 · UniProt A8K1V4

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