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Discovery of the second generation ror gamma inhibitors composed of an azole scaffold.

Analyse Discovery of the second generation ror gamma inhibitors composed of an azole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IVX
Type: protein
Length: 957 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma; Nuclear receptor corepressor 2
UniProt: P51449, Q9Y618
Ligands: AYO
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 72% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, G	Nuclear receptor ror-gamma	protein	227	71% helix, 4% strand	P51449
B, F	Nuclear receptor corepressor 2	protein	14	79% helix, 0% strand	Q9Y618
D	Nuclear receptor corepressor 2	protein	9	78% helix, 0% strand	Q9Y618
E	Nuclear receptor ror-gamma	protein	226	71% helix, 4% strand	P51449
H	Nuclear receptor corepressor 2	protein	13	85% helix, 0% strand	Q9Y618

Ligands and binding sites

AYO · (4S)-4-[4'-cyclopropyl-5-(2,2-dimethylpropyl)[3,5'-bi-1,2-oxazol]-3'-yl]-6-[(2,4-dichlorophenyl)amino]-6-oxohexanoic acid · ligand · 4 copies · chains A, C, E, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	382	0.83	0.91	32	AYO
2	421	0.81	0.89	37	AYO
3	437	0.81	0.88	32	AYO
4	446	0.80	0.88	38	AYO
5	859	0.78	0.81	81	empty

Interfaces

8 interfaces between chains.

E–F · 741 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 725 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 714 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 513 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 507 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6IVX · Discovery of the Second Generation ROR gamma Inhibitors Composed of an Azole Scaffold. · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain D against A, TM-score 0.86

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 Q9Y618
Elsewhere: RCSB PDB 6IVX · PDBe 6IVX · UniProt P51449 · UniProt Q9Y618

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