6ES0: Kinase domain of human RIPK2

Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor CS-R35. Determined by X-ray diffraction at 2.38 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,901
Mol. weight: 73.75 kDa
Ligands: BW8
Released: 21 Feb 2018

Explore 6ES0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ES0 contains 33 α-helices and 22 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
α-helix	10-11	2
β-strand	12	1	2
α-helix	15-17	3
β-strand	18-23	6	2
β-strand	32-37	6	2
β-strand	43-48	6	2
α-helix	55-56	2
α-helix	57-72	16
β-strand	78	1	3
α-helix	79-80	2
β-strand	81-86	6	2
β-strand	91-96	6	2
β-strand	102	1	3
α-helix	103-108	6
α-helix	118-136	19
α-helix	141-142	2
α-helix	149-151	3
β-strand	152-154	3	3
β-strand	160-162	3	3
α-helix	195-197	3
α-helix	211-224	14
α-helix	235-243	9
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-295	13
α-helix	300-312	13

Chain B: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
α-helix	10-11	2
β-strand	12	1	4
α-helix	15-17	3
β-strand	18-23	6	4
β-strand	32-37	6	4
β-strand	43-48	6	4
α-helix	63-72	10
β-strand	78	1	5
α-helix	79-80	2
β-strand	81-86	6	4
β-strand	91-96	6	4
β-strand	102	1	5
α-helix	103-108	6
α-helix	118-136	19
α-helix	149-151	3
β-strand	152-154	3	5
β-strand	160-162	3	5
α-helix	195-197	3
α-helix	202-205	4
α-helix	210-224	15
α-helix	235-244	10
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-294	12
α-helix	299-313	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, B	protein	317	Homo sapiens	O43353 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ES0_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, B)
SMGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSER
KDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPL
RFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLSQSRS
SKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMY
SVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEI
TFLEAVIQLKKTKLQSV

Ligands and cofactors

ID	Name	Formula	Copies
BW8	2-[2-fluoranyl-4-[[2-fluoranyl-4-[2-(methylcarbamoyl)pyridin-4-yl]oxy-phenyl]ca…	C22 H18 F2 N4 O5 S	2

Primary citation

Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors. Suebsuwong, C., Pinkas, D.M., Ray, S.S. et al. Bioorg Med Chem Lett (2018) 28:577-583. DOI 10.1016/j.bmcl.2018.01.044 · 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
8X2O 2.26 Å, RIPK2 in complex with K252
7OBT 2.3 Å, Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide and stabilizer…
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

Browse structure collections

About this viewer

MolViewer shows 6ES0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.