5HX6: RIP1 kinase with a benzo[b][1,4]oxazepin-4-one

Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one. Determined by X-ray diffraction at 2.23 Å resolution. Released 2 Mar 2016.

Method: X-ray diffraction
Resolution: 2.23 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,198
Mol. weight: 69.95 kDa
Ligands: 65U
Released: 2 Mar 2016

Explore 5HX6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HX6 contains 30 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: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	1
α-helix	14-16	3
β-strand	17-19	3	1
β-strand	22-23	2	1
β-strand	31-36	6	1
β-strand	40-49	10	1
α-helix	57-68	12
β-strand	75	1	2
β-strand	78-83	6	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	141-143	3
β-strand	144-146	3	2
β-strand	152-154	3	2
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	278-292	15

Chain B: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	3
β-strand	32-36	5	3
β-strand	40-48	9	3
α-helix	54-68	15
β-strand	75	1	4
β-strand	78-84	7	3
β-strand	87-93	7	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	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	303	Homo sapiens	Q13546 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5HX6_1 Receptor-interacting serine/threonine-protein kinase 1 (chains A, B)
MDYKDDDDKMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGP
NCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTP
LSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNE
EHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENA
IAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLS
QLE

Ligands and cofactors

ID	Name	Formula	Copies
65U	5-benzyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-1,2-o…	C21 H19 N3 O4	2

Primary citation

DNA-Encoded Library Screening Identifies Benzo[b][1,4]oxazepin-4-ones as Highly Potent and Monoselective Receptor Interacting Protein 1 Kinase Inhibitors. Harris, P.A., King, B.W., Bandyopadhyay, D. et al. J Med Chem (2016) 59:2163-2178. DOI 10.1021/acs.jmedchem.5b01898 · 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
4ITH 2.25 Å, Crystal structure of RIP1 kinase in complex with necrostatin-1 analog
9GTG 2.25 Å, RIPK1 in complex with AZ"902

Browse structure collections

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