8I2N: The RIPK1 kinase domain

The RIPK1 kinase domain in complex with QY7-2B compound. Determined by X-ray diffraction at 2.29 Å resolution. Released 31 Jan 2024.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,415
Mol. weight: 67.89 kDa
Ligands: O4U
Released: 31 Jan 2024

Explore 8I2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I2N contains 39 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: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	1
α-helix	14-16	3
β-strand	17-22	6	1
β-strand	31-36	6	1
β-strand	40-49	10	1
α-helix	57-67	11
β-strand	75	1	2
α-helix	76-77	2
β-strand	78-84	7	1
β-strand	87-93	7	1
β-strand	99	1	2
α-helix	100-104	5
α-helix	109-111	3
α-helix	112-131	20
α-helix	134-136	3
α-helix	141-143	3
β-strand	144-146	3	2
β-strand	152-154	3	2
α-helix	163-169	7
α-helix	195-197	3
α-helix	203-205	3
α-helix	207-223	17
α-helix	234-242	9
α-helix	249-251	3
α-helix	258-267	10
α-helix	272-274	3
α-helix	276-277	2
α-helix	278-288	11
α-helix	289-293	5

Chain B: 20 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	3
α-helix	14-16	3
β-strand	17	1	3
β-strand	32-36	5	3
β-strand	40-48	9	3
α-helix	57-67	11
β-strand	75	1	4
α-helix	76-77	2
β-strand	78-84	7	3
β-strand	87-92	6	3
α-helix	93-95	3
β-strand	98-99	2	4
α-helix	100-105	6
α-helix	109-111	3
α-helix	112-131	20
α-helix	141-143	3
β-strand	144-146	3	4
β-strand	152-154	3	4
α-helix	163-168	6
α-helix	188-192	5
α-helix	195-197	3
α-helix	204-205	2
α-helix	207-223	17
α-helix	234-242	9
α-helix	249-251	3
α-helix	258-267	10
α-helix	272-274	3
α-helix	276-277	2
α-helix	278-288	11
α-helix	289-293	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 1	A, B	protein	294	Homo sapiens	Q13546 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8I2N_1 Receptor-interacting serine/threonine-protein kinase 1 (chains A, B)
MQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEAL
LEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIIL
EIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVD
GTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMA
IKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE

Ligands and cofactors

ID	Name	Formula	Copies
O4U	~{N}-methyl-1-[4-[[[1-methyl-5-(phenylmethyl)pyrazol-3-yl]carbonylamino]methyl]…	C28 H26 N6 O2	2

Primary citation

Structure-based development of potent and selective type-II kinase inhibitors of RIPK1. Qin, Y., Li, D., Qi, C. et al. Acta Pharm Sin B (2024) 14:319-334. DOI 10.1016/j.apsb.2023.10.021 · PubMed

Other PDB entries of the same protein (UniProt Q13546 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ZMZ 1.4 Å, Amyloid core of RIP1
6AC5 1.45 Å, Crystal structure of RIPK1 death domain GlcNAcylated by EPEC effector NleB
4ITJ 1.8 Å, Crystal structure of RIP1 kinase in complex with necrostatin-4
6NW2 2.0 Å, Structure of human RIPK1 kinase domain in complex with compound 11
7FD0 2.0 Å, Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor
24IB 2.05 Å, Crystal structure of human RIPK1 kinase domain in complex with compound HR10
9Q31 2.05 Å, RIP1 kinase domain in complex with GDC-8264
6NYH 2.1 Å, Structure of human RIPK1 kinase domain in complex with GNE684
9GTY 2.15 Å, RIPK1 in complex with AZ"320
7FCZ 2.21 Å, Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor
5HX6 2.23 Å, Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one
4ITH 2.25 Å, Crystal structure of RIP1 kinase in complex with necrostatin-1 analog

Browse structure collections

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