MolNFT v1 · #131312 · protein

Ligand binding to farnesoid-X-receptor

5Q1F · Bile acid receptor: “Ligand binding to farnesoid-X-receptor”. X-ray diffraction, 1 ligand (9NJ), 5 pockets (best druggability 0.86). MolNFT v1 #131312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Q1F
Type: protein
Length: 479 residues
Chains: 4
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: 9NJ
Pockets: 5 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bile acid receptor	protein	229	70% helix, 0% strand	Q96RI1
B	Coactivator peptide src-1 HD3	protein	11	73% helix, 0% strand	A8K1V4
C	Bile acid receptor	protein	229	72% helix, 0% strand	Q96RI1
D	Coactivator peptide src-1 HD3	protein	10	80% helix, 0% strand	A8K1V4

Ligands and binding sites

9NJ · Trans-4-({(2S)-2-cyclohexyl-2-[2-(2,6-dimethoxypyridin-3-yl)-5-fluoro-1H-benzimidazol-1-yl]acetyl}amino) cyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	388	0.86	0.94	38	9NJ
2	551	0.81	0.87	61	9NJ
3	94	0.37	0.76	17	empty
4	96	0.37	0.75	17	empty
5	50	0.31	0.77	12	empty

Interfaces

3 interfaces between chains.

C–D · 594 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 574 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 131 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5Q1F · 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 5Q1F · PDBe 5Q1F · UniProt Q96RI1 · UniProt A8K1V4

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