6UL8: PDB entry 6UL8

RIP2 kinase catalytic domain complex with (5S,6S,8R)-2-(benzo[d]thiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide. Determined by X-ray diffraction at 2.68 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,631
Mol. weight: 71.14 kDa
Ligands: CA, Q9J
Released: 4 Dec 2019

Explore 6UL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UL8 contains 32 α-helices and 27 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, 14 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	18-25	8	2
β-strand	31-37	7	2
β-strand	43-48	6	2
α-helix	57-72	16
β-strand	75	1	3
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
β-strand	143	1	4
α-helix	149-151	3
β-strand	152-154	3	3
β-strand	160-162	3	3
β-strand	169	1	4
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	283-294	12
α-helix	299-307	9

Chain B: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
α-helix	10-11	2
β-strand	12	1	5
α-helix	15-17	3
β-strand	18-25	8	5
β-strand	31-37	7	5
β-strand	43-48	6	5
α-helix	57-72	16
β-strand	78	1	6
α-helix	79-80	2
β-strand	81-86	6	5
β-strand	91-96	6	5
β-strand	102	1	6
α-helix	103-108	6
α-helix	118-136	19
β-strand	143	1	7
α-helix	149-151	3
β-strand	152-154	3	6
β-strand	160-162	3	6
β-strand	169	1	7
α-helix	195-197	3
α-helix	202-205	4
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	299-309	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, B	protein	306	Homo sapiens	O43353 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6UL8_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, B)
AISSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSERKDVL
REAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRI
LHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLCKWRMMSLSQSRSSKSA
PEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQ
GHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLE
AVIQLK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
Q9J	(5S,6S,8R)-2-(1,3-benzothiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methan…	C17 H17 N5 O2 S	2

Primary citation

Discovery of Pyrazolocarboxamides as Potent and Selective Receptor Interacting Protein 2 (RIP2) Kinase Inhibitors. Haffner, C.D., Charnley, A.K., Aquino, C.J. et al. ACS Med Chem Lett (2019) 10:1518-1523. DOI 10.1021/acsmedchemlett.9b00141 · 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…
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…

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