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Structure of the kinase domain of human RIPK2 in complex with ponatinib

Analyse Structure of the kinase domain of human RIPK2 in complex with ponatinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C8B
Type: protein
Length: 560 residues
Chains: 2
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: 0LI
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	279	43% helix, 17% strand	O43353
B	Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2)	protein	281	44% helix, 16% strand	O43353

Ligands and binding sites

0LI · 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl) phenyl}benzamide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.81	0.82	71	empty
2	419	0.70	0.81	50	0LI
3	327	0.69	0.82	36	0LI
4	81	0.37	0.76	16	empty
5	85	0.35	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1481 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4C8B · Structure of the kinase domain of human RIPK2 in complex with ponatinib · the same entry in another collection · chain A against A, TM-score 1.00
O43353 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 4C8B · PDBe 4C8B · UniProt O43353

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