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Ligand complex of rorg lbd

Analyse Ligand complex of rorg lbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NIB
Type: protein
Length: 262 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor ror-gamma; The tethered SRC2-2 peptide
UniProt: P51449
Ligands: 8Y5, NA
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor ror-gamma	protein	252	73% helix, 4% strand	P51449
C	The tethered SRC2-2 peptide	protein	10	70% helix, 0% strand	—

Ligands and binding sites

8Y5 · ~{N}-[4-[2-[(3-cyanophenyl)methoxy]pyridin-3-yl]thiophen-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide · ligand · chains A
NA · Sodium ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.81	0.91	38	8Y5
2	75	0.41	0.79	15	NA
3	72	0.39	0.78	17	empty
4	72	0.31	0.74	14	empty

Interfaces

1 interface between chains.

A–C · 487 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5NIB · Ligand complex of RORg LBD · 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 P51449
Elsewhere: RCSB PDB 5NIB · PDBe 5NIB · UniProt P51449

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