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Structure of cinaciguat (bay 58-2667) bound to nostoc H-nox domain

Analyse Structure of cinaciguat (bay 58-2667) bound to nostoc H-nox domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L6J
Type: protein
Length: 364 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ALR2278 protein
UniProt: Q8YUQ7
Ligands: Z90
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ALR2278 protein	protein	182	55% helix, 15% strand	Q8YUQ7

Ligands and binding sites

Z90 · 4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl) benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.84	0.86	94	Z90
2	370	0.84	0.92	36	Z90
3	87	0.52	0.84	30	empty
4	54	0.50	0.86	19	empty

Interfaces

1 interface between chains.

A–B · 640 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3L6J · Structure of cinaciguat (bay 58-2667) bound to nostoc H-NOX domain · 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 Q8YUQ7
Elsewhere: RCSB PDB 3L6J · PDBe 3L6J · UniProt Q8YUQ7

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