7XMK: Human RIPK1 kinase domain

Crystal structure of human RIPK1 kinase domain in complex with compound SKLB923. Determined by X-ray diffraction at 2.38 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,333
Mol. weight: 68.18 kDa
Ligands: GO4
Released: 26 Apr 2023

Explore 7XMK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XMK contains 35 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: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	14-16	3
β-strand	17	1	1
β-strand	31-36	6	1
β-strand	40-48	9	1
α-helix	54-56	3
α-helix	57-68	12
β-strand	75	1	2
α-helix	76-77	2
β-strand	78-83	6	1
β-strand	88-92	5	1
β-strand	99	1	2
α-helix	100-105	6
α-helix	112-131	20
α-helix	141-143	3
β-strand	144-146	3	2
β-strand	152-154	3	2
α-helix	163-170	8
α-helix	195-197	3
α-helix	203-205	3
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	278-288	11
α-helix	289-293	5

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	3
α-helix	14-16	3
β-strand	17-22	6	3
β-strand	32-36	5	3
β-strand	40-46	7	3
α-helix	57-67	11
β-strand	75	1	4
α-helix	76-77	2
β-strand	78-84	7	3
β-strand	87-93	7	3
β-strand	99	1	4
α-helix	100-105	6
α-helix	112-131	20
α-helix	141-143	3
β-strand	144-146	3	4
β-strand	152-154	3	4
α-helix	163-167	5
α-helix	195-197	3
α-helix	204-205	2
α-helix	207-223	17
α-helix	235-243	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

>7XMK_1 Receptor-interacting serine/threonine-protein kinase 1 (chains A, B)
MQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEAL
LEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIIL
EIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVD
GTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMA
IKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE

Ligands and cofactors

ID	Name	Formula	Copies
GO4	5-[2-(cyclopropylcarbonylamino)-[1,2,4]triazolo[1,5-a]pyridin-7-yl]-N-[(1S)-1-(…	C28 H25 F N6 O2	2

Water and common crystallization additives (IOD) are not listed.

Primary citation

From Hit to Lead: Structure-Based Optimization of Novel Selective Inhibitors of Receptor-Interacting Protein Kinase 1 (RIPK1) for the Treatment of Inflammatory Diseases. Zhang, L., Li, Y., Tian, C. et al. J Med Chem (2024) 67:754-773. DOI 10.1021/acs.jmedchem.3c02102 · 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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