9GTG: RIPK1

RIPK1 in complex with AZ"902. Determined by X-ray diffraction at 2.25 Å resolution. Released 2 Jul 2025.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,225
Mol. weight: 72.59 kDa
Ligands: RCM, A1IPG
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

9GTG contains 31 α-helices and 23 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
α-helix	14-16	3
β-strand	17	1	1
β-strand	24	1	2
β-strand	30	1	2
β-strand	33-36	4	1
β-strand	40-45	6	1
α-helix	57-68	12
β-strand	75	1	3
β-strand	78-83	6	1
β-strand	88-92	5	1
β-strand	98-99	2	3
α-helix	100-104	5
α-helix	109-111	3
α-helix	112-131	20
α-helix	141-143	3
β-strand	144-146	3	3
β-strand	152-154	3	3
α-helix	164-167	4
α-helix	189-192	4
α-helix	195-197	3
α-helix	204-205	2
α-helix	207-223	17
α-helix	234-243	10
α-helix	249-251	3
α-helix	258-267	10
α-helix	272-274	3
α-helix	276-277	2
α-helix	278-293	16

Chain B: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	4
β-strand	17	1	4
β-strand	22	1	4
β-strand	31-36	6	4
β-strand	40-45	6	4
α-helix	60-67	8
β-strand	75	1	5
β-strand	78-83	6	4
β-strand	88-92	5	4
β-strand	98-99	2	5
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	5
β-strand	152-154	3	5
α-helix	190-192	3
α-helix	195-197	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	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	313	Homo sapiens	Q13546 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9GTG_1 Receptor-interacting serine/threonine-protein kinase 1 (chains A, B)
MGHHHHHHGGGENLYFQGSMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGL
MIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLM
HVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLAS
FKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAI
FANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGI
EEKFRPFYLSQLE

Ligands and cofactors

ID	Name	Formula	Copies
RCM	(5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione	C13 H12 Cl N3 O2	2
A1IPG	~{N}-[[(3~{S})-1-ethanoylpyrrolidin-3-yl]methyl]-~{N}-methyl-4-quinolin-7-yl-be…	C23 H25 N3 O3 S	2

Primary citation

Discovery and Validation of a Novel Class of Necroptosis Inhibitors Targeting RIPK1. Soday, L., Seripracharat, C., Gray, J.L. et al. ACS Chem Biol (2025) 20:1527-1543. DOI 10.1021/acschembio.5c00112 · 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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