8X2O: RIPK2

RIPK2 in complex with K252. Determined by X-ray diffraction at 2.26 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,541
Mol. weight: 73.56 kDa
Ligands: 6IL
Released: 13 Nov 2024

Explore 8X2O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X2O contains 30 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12	1	1
α-helix	15-17	3
β-strand	18-26	9	1
β-strand	31-37	7	1
β-strand	43-48	6	1
α-helix	58-72	15
β-strand	78	1	2
α-helix	79-80	2
β-strand	81-87	7	1
β-strand	90-96	7	1
β-strand	102	1	2
α-helix	103-108	6
α-helix	118-136	19
β-strand	142-143	2	3
α-helix	149-151	3
β-strand	152-154	3	2
β-strand	160-162	3	2
β-strand	169-170	2	3
α-helix	195-197	3
α-helix	210-224	15
α-helix	235-243	9
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-294	12
α-helix	299-315	17

Chain B: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	4
α-helix	15-17	3
β-strand	18-26	9	4
β-strand	31-37	7	4
β-strand	43-48	6	4
α-helix	58-72	15
β-strand	78	1	5
α-helix	79-80	2
β-strand	81-87	7	4
β-strand	90-96	7	4
β-strand	102	1	5
α-helix	103-108	6
α-helix	118-136	19
α-helix	141	1
β-strand	142-143	2	6
α-helix	149-151	3
β-strand	152-154	3	5
β-strand	160-162	3	5
β-strand	169-170	2	6
α-helix	195-197	3
α-helix	210-224	15
α-helix	235-243	9
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-294	12
α-helix	299-315	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, B	protein	316	Homo sapiens	O43353 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8X2O_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, B)
MNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSER
KDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPL
RFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSRS
SKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMY
SVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEI
TFLEAVIQLKKTKLQS

Ligands and cofactors

ID	Name	Formula	Copies
6IL	~{N}-[(1~{R})-4-[4-[(6-fluoranyl-1,3-benzothiazol-5-yl)amino]thieno[2,3-d]pyrim…	C23 H20 F N5 O S2	2

Primary citation

CMD-OPT model enables the discovery of a potent and selective RIPK2 inhibitor as preclinical candidate for the treatment of acute liver injury. Chen, Y., Yuan, X., Yan, W. et al. Acta Pharm Sin B (2025) 15:3708-3724. DOI 10.1016/j.apsb.2025.05.003 · PubMed

Other PDB entries of the same protein (UniProt O43353 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OBS 1.8 Å, Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide
9F3V 1.94 Å, RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor
5NG0 2.0 Å, Structure of RIP2K(L294F) with bound AMPPCP
7OBT 2.3 Å, Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide and stabilizer…
6ES0 2.38 Å, Crystal structure of the kinase domain of human RIPK2 in complex with the activation…
5AR2 2.44 Å, RIP2 Kinase Catalytic Domain (1 - 310)
5J7B 2.53 Å, The identification and pharmacological characterization of…
6HMX 2.53 Å, RIP2 Kinase Catalytic Domain complex with N(4,5dimethyl1Hpyrazol3yl)7methoxy6(2methylprop…
6SZJ 2.53 Å, RIP2 Kinase Catalytic Domain complex with 5amino1tertbutyl3(3methoxyphenyl)1H…
5NG3 2.6 Å, Structure of inactive kinase RIP2K(K47R)
6RNA 2.62 Å, RIP2 Kinase Catalytic Domain complex with 2({4[(1,3benzothiazol5yl)amino]6(2methylpropane…
5AR5 2.66 Å, RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole

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