Research workbench
Hrxralpha & mlxralpha with an indole pharmacophore, SB786875
Analyse Hrxralpha & mlxralpha with an indole pharmacophore, SB786875 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FC6
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; NR1H3 protein
- UniProt
- P19793, Q91X41
- Ligands
- REA, LX2
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 207 | 73% helix, 3% strand | P19793 |
| B, D | NR1H3 protein | protein | 241 | 69% helix, 4% strand | Q91X41 |
| C | Retinoic acid receptor rxr-alpha | protein | 202 | 70% helix, 3% strand | P19793 |
Ligands and binding sites
- REA · Retinoic acid · ligand · 2 copies · chains A, C
- LX2 · [4-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)-1H-indol-1-yl]acetic acid · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.84 | 0.91 | 52 | LX2 |
| 2 | 427 | 0.84 | 0.91 | 52 | LX2 |
| 3 | 330 | 0.81 | 0.91 | 47 | REA |
| 4 | 1118 | 0.77 | 0.79 | 91 | empty |
| 5 | 499 | 0.74 | 0.82 | 50 | REA |
Interfaces
5 interfaces between chains.
- A–B · 1659 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1538 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 737 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 686 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3FC6 · hRXRalpha & mLXRalpha with an indole Pharmacophore, SB786875 · the same entry in another collection · chain B against B, 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 P19793
- Every structure of UniProt Q91X41
- Elsewhere: RCSB PDB 3FC6 · PDBe 3FC6 · UniProt P19793 · UniProt Q91X41
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