Research workbench
Human LRH1 lbd bound to GR470
Analyse Human LRH1 lbd bound to GR470 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PLZ
- Type
- protein
- Length
- 495 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ftz-F1 related protein; Nuclear receptor coactivator 2
- UniProt
- Q9UEC0, Q15596
- Ligands
- 470
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ftz-F1 related protein | protein | 231 | 71% helix, 3% strand | Q9UEC0 |
| C, D | Nuclear receptor coactivator 2 | protein | 12 | 67% helix, 0% strand | Q15596 |
| B | Ftz-F1 related protein | protein | 240 | 72% helix, 3% strand | Q9UEC0 |
Ligands and binding sites
- 470 · (3aS,6aR)-5-[(4E)-oct-4-en-4-yl]-N,4-diphenyl-2,3,6,6a-tetrahydropentalen-3a(1H)-amine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 345 | 0.87 | 0.95 | 34 | 470 |
| 2 | 376 | 0.86 | 0.94 | 38 | 470 |
| 3 | 1065 | 0.78 | 0.80 | 70 | empty |
| 4 | 161 | 0.69 | 0.88 | 25 | empty |
| 5 | 180 | 0.69 | 0.87 | 24 | EDO |
Interfaces
3 interfaces between chains.
- B–D · 687 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 622 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3PLZ · Human LRH1 LBD bound to GR470 · 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 Q9UEC0
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3PLZ · PDBe 3PLZ · UniProt Q9UEC0 · UniProt Q15596
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