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Non peptide agonist pf-06882961, bound to glucagon-like peptide-1 (glp-1) receptor

Analyse Non peptide agonist pf-06882961, bound to glucagon-like peptide-1 (glp-1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X1A
Type: protein
Length: 1,262 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
UniProt: P63092, P62873, P59768, P43220
Ligands: UK4
Pockets: 17 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	351	52% helix, 11% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	7% helix, 44% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	57	40% helix, 0% strand	P59768
N	NANOBODY35	protein	126	2% helix, 43% strand	—
R	Glucagon-like peptide 1 receptor	protein	390	62% helix, 3% strand	P43220

Ligands and binding sites

UK4 · 2-[(4-{6-[(4-cyano-2-fluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1-{[(2S)-oxetan-2-yl]methyl}-1H-benzimidazole-6-carboxylic acid · ligand · chains R

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.85	0.88	67	UK4
2	666	0.81	0.86	51	empty
3	712	0.76	0.81	68	empty
4	1085	0.76	0.78	80	empty
5	943	0.75	0.78	69	empty

Interfaces

6 interfaces between chains.

B–G · 2214 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1518 Å² buried · 22 hydrogen bonds · protein-protein
A–R · 1045 Å² buried · 10 hydrogen bonds · protein-protein
A–N · 874 Å² buried · 16 hydrogen bonds · protein-protein
B–N · 577 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6X1A · Non peptide agonist PF-06882961, bound to Glucagon-Like peptide-1 (GLP-1) Receptor · the same entry in another collection · chain R against R, TM-score 1.00
P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.88
P43220 · AlphaFold monomer V2.0 prediction for glucagon-like peptide 1 receptor (P43220) · a predicted model of the same protein · chain R against A, TM-score 0.81

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 P63092
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt P43220
Elsewhere: RCSB PDB 6X1A · PDBe 6X1A · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt P43220

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