MolNFT v1 · #128543 · protein
Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
5NTW · Nuclear receptor ror-gamma: “Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural…”. X-ray diffraction, 1 ligand (98N), 16 pockets (best druggability 0.90). MolNFT v1 #128543 on…
- PDB
- 5NTW
- Type
- protein
- Length
- 1,017 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor-interacting protein 1
- UniProt
- P51449, P48552
- Ligands
- 98N
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nuclear receptor ror-gamma | protein | 245 | 72% helix, 4% strand | P51449 |
| P, R, S | Nuclear receptor-interacting protein 1 | protein | 9 | 67% helix, 0% strand | P48552 |
| Q | Nuclear receptor-interacting protein 1 | protein | 10 | 60% helix, 0% strand | P48552 |
Ligands and binding sites
- 98N · (S)-N-((5-(ethylsulfonyl)pyridin-2-yl)methyl)-7-isopropyl-6-(((1R,4S)-4-(trifluoromethyl)cyclohexyl) methyl)-6,7-dihydro-5H-pyrrolo[3,4-b]pyridine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.90 | 0.92 | 107 | 98N |
| 2 | 389 | 0.84 | 0.92 | 37 | 98N |
| 3 | 396 | 0.84 | 0.91 | 41 | 98N |
| 4 | 892 | 0.73 | 0.77 | 74 | empty |
| 5 | 421 | 0.63 | 0.77 | 38 | empty |
Interfaces
10 interfaces between chains.
- A–C · 962 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 529 Ų buried · 6 hydrogen bonds · protein-protein
- D–S · 514 Ų buried · 4 hydrogen bonds · protein-protein
- B–Q · 513 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NTW · Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding… · the same entry in another collection · chain S against S, TM-score 1.00
- P48552 · AlphaFold monomer V2.0 prediction for nuclear receptor-interacting protein 1 (P48552) · a predicted model of the same protein · chain P against A, TM-score 0.82
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 P51449
- Every structure of UniProt P48552
- Elsewhere: RCSB PDB 5NTW · PDBe 5NTW · UniProt P51449 · UniProt P48552
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