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Ligand binding domain of ppargamma complexed with a benzimidazole partial agonist

Analyse Ligand binding domain of ppargamma complexed with a benzimidazole partial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S9S
Type: protein
Length: 268 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisome proliferator-activated receptor gamma; Nuclear receptor coactivator 1
UniProt: P37231, Q15788
Ligands: M0T
Pockets: 1 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisome proliferator-activated receptor gamma	protein	258	63% helix, 5% strand	P37231
B	Nuclear receptor coactivator 1	protein	10	70% helix, 0% strand	Q15788

Ligands and binding sites

M0T · 1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.83	0.91	48	M0T

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3S9S · Ligand binding domain of PPARgamma complexed with a benzimidazole partial agonist · 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 P37231
Every structure of UniProt Q15788
Elsewhere: RCSB PDB 3S9S · PDBe 3S9S · UniProt P37231 · UniProt Q15788

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