MolNFT v1 · #142492 · protein
Crystal structure of human FXR/RXR-lbd heterodimer bound to HNC143 and 9CRA and SRC1
6A5Y · Bile acid receptor: “Crystal structure of human FXR/RXR-lbd heterodimer bound to HNC143 and 9CRA and SRC1”. X-ray diffraction, 4 ligands (9R0, 9CR, SO4), 7 pockets (best druggability 0.83). MolNFT v1 #142492 on GenesisL1: 3D…
- PDB
- 6A5Y
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; Nuclear receptor coactivator 1; Retinoic acid receptor rxr-alpha
- UniProt
- Q96RI1, B5MCN7, P19793
- Ligands
- 9R0, 9CR, SO4, PO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 228 | 73% helix, 0% strand | Q96RI1 |
| B | Nuclear receptor coactivator 1 | protein | 10 | 60% helix, 0% strand | B5MCN7 |
| D | Retinoic acid receptor rxr-alpha | protein | 211 | 72% helix, 3% strand | P19793 |
| F | Nuclear receptor coactivator 1 | protein | 13 | 62% helix, 0% strand | B5MCN7 |
Ligands and binding sites
- 9R0 · 2-[2-[[3-[2,6-bis(chloranyl)phenyl]-5-cyclopropyl-1,2-oxazol-4-yl]methoxy]-6-azaspiro[3.4]octan-6-yl]-1,3-benzothiazole-6-carboxylic acid · ligand · chains A
- 9CR · (9cis)-retinoic acid · ligand · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- PO4 · Phosphate ion · ion · chains D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.83 | 0.93 | 41 | 9CR |
| 2 | 353 | 0.81 | 0.90 | 38 | 9R0 |
| 3 | 463 | 0.62 | 0.76 | 36 | empty |
| 4 | 360 | 0.61 | 0.78 | 29 | SO4 |
| 5 | 119 | 0.58 | 0.85 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1102 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 659 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 592 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6A5Y · Crystal structure of human FXR/RXR-LBD heterodimer bound to HNC143 and 9cRA and SRC1 · 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 B5MCN7
- Every structure of UniProt P19793
- Elsewhere: RCSB PDB 6A5Y · PDBe 6A5Y · UniProt Q96RI1 · UniProt B5MCN7 · UniProt P19793
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