MolNFT v1 · #152792 · protein
Crystal structure of fxr in complex with agonist XJ034
6ITM · Bile acid receptor: “Crystal structure of fxr in complex with agonist XJ034”. X-ray diffraction, 1 ligand (AWL), 7 pockets (best druggability 0.85). MolNFT v1 #152792 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ITM
- Type
- protein
- Length
- 477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; HD3 peptide from nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q96RI1, Q15788
- Ligands
- AWL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 225 | 75% helix, 0% strand | Q96RI1 |
| B, D | HD3 peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 12 | 67% helix, 0% strand | Q15788 |
| C | Bile acid receptor | protein | 228 | 76% helix, 0% strand | Q96RI1 |
Ligands and binding sites
- AWL · 1-adamantyl-[4-(5-chloranyl-2-methyl-phenyl)piperazin-1-yl]methanone · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.85 | 0.96 | 28 | AWL |
| 2 | 216 | 0.84 | 0.96 | 32 | AWL |
| 3 | 301 | 0.55 | 0.75 | 30 | empty |
| 4 | 74 | 0.50 | 0.84 | 18 | empty |
| 5 | 179 | 0.47 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 648 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 601 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 597 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6ITM · Crystal structure of FXR in complex with agonist XJ034 · 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 Q15788
- Elsewhere: RCSB PDB 6ITM · PDBe 6ITM · UniProt Q96RI1 · UniProt Q15788
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