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Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases.

Analyse Identification of potent and selective RIPK2 inhibitors for the treatment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W5O
Type: protein
Length: 4,399 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor-interacting SERINE/THREONINE-protein kinase 2
EC: 2.7.11.1, 2.7.10.2
UniProt: O43353
Ligands: 9XA
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, P	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	275	39% helix, 18% strand	O43353
M	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	276	39% helix, 18% strand	O43353
N	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	272	37% helix, 18% strand	O43353
O	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	276	37% helix, 18% strand	O43353

Ligands and binding sites

9XA · 4-{6-(tert-butylsulfonyl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]imidazo[1,2-a]pyridin-3-yl}-6-chloropyridin-2-amine · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.84	0.86	83	empty
2	880	0.84	0.85	90	empty
3	634	0.84	0.88	72	empty
4	693	0.84	0.87	67	empty
5	757	0.83	0.86	79	empty

Interfaces

27 interfaces between chains.

O–P · 1922 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1890 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1884 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 1843 Å² buried · 17 hydrogen bonds · protein-protein
M–N · 1842 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5W5O · Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory… · the same entry in another collection · chain P against P, 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 O43353
Elsewhere: RCSB PDB 5W5O · PDBe 5W5O · UniProt O43353

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