9F3V: PDB entry 9F3V

RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor. Determined by X-ray diffraction at 1.94 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,738
Mol. weight: 74.22 kDa
Ligands: A1H90
Released: 6 Nov 2024

Explore 9F3V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F3V contains 33 α-helices and 20 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: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
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	57-70	14
β-strand	78	1	2
α-helix	79-80	2
β-strand	81-86	6	1
β-strand	91-96	6	1
β-strand	102	1	2
α-helix	103-108	6
α-helix	118-137	20
α-helix	141-142	2
α-helix	149-151	3
β-strand	152-154	3	2
β-strand	160-162	3	2
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	283-295	13
α-helix	299-313	15

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
β-strand	12	1	3
α-helix	15-17	3
β-strand	18-26	9	3
β-strand	30-37	8	3
β-strand	43-49	7	3
α-helix	57-70	14
β-strand	78	1	4
α-helix	79-80	2
β-strand	81-86	6	3
β-strand	91-96	6	3
β-strand	102	1	4
α-helix	103-108	6
α-helix	118-137	20
α-helix	141-142	2
α-helix	149-151	3
β-strand	152-154	3	4
β-strand	160-162	3	4
α-helix	166-168	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	283-295	13
α-helix	299-313	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, B	protein	320	Homo sapiens	O43353 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9F3V_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, B)
GAMAMNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLL
DSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDV
AWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLS
QSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPL
QIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRT
FEEITFLEAVIQLKKTKLQS

Ligands and cofactors

ID	Name	Formula	Copies
A1H90	N-[2,4-bis(chloranyl)-5-methoxy-phenyl]-7-[2-(diethylamino)ethoxy]-6-methoxy-qu…	C22 H26 Cl2 N4 O3	2

Primary citation

4-Anilinoquinazoline Derivatives as the First Potent NOD1-RIPK2 Signaling Pathway Inhibitors at the Nanomolar Range. Barczyk, A., Six, P., Rivoal, M. et al. J Med Chem (2024) 67:19304-19322. DOI 10.1021/acs.jmedchem.4c01713 · 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
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…
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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