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Structural basis for a pentacyclic oleanane-type triterpenoid as a ligand of fxr

Analyse Structural basis for a pentacyclic oleanane-type triterpenoid as a ligand of fxr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WZX
Type: protein
Length: 445 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; SRC2-3 peptide from nuclear receptor coactivator 2
UniProt: Q96RI1, Q15596
Ligands: 7VX
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bile acid receptor	protein	210	67% helix, 0% strand	Q96RI1
B	Bile acid receptor	protein	212	66% helix, 0% strand	Q96RI1
C	SRC2-3 peptide from nuclear receptor coactivator 2	protein	12	67% helix, 0% strand	Q15596
D	SRC2-3 peptide from nuclear receptor coactivator 2	protein	11	64% helix, 0% strand	Q15596

Ligands and binding sites

7VX · (4ar,6ar,6as,6bs,8as,9r,12ar,14br)-2,2,6A,6B,9,12A-hexamethyl-10-oxidanylidene-1,3,4,5,6,6A,7,8,8A,9,11, 12,13,14B-tetradecahydropicene-4A-carboxylic acid · ligand · 2 copies · chains A, B
BU3 · (R,R)-2,3-butanediol · additive · 3 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.83	0.84	92	empty
2	460	0.83	0.90	39	7VX
3	496	0.82	0.88	42	7VX
4	85	0.59	0.88	21	empty
5	54	0.35	0.79	15	empty

Interfaces

3 interfaces between chains.

A–B · 1084 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 572 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 548 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5WZX · Structural basis for a pentacyclic oleanane-type triterpenoid as a ligand of 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 Q15596
Elsewhere: RCSB PDB 5WZX · PDBe 5WZX · UniProt Q96RI1 · UniProt Q15596

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