5HX6

Crystal structure of RIP1 kinase with a benzo[b][1,4]oxazepin-4-one

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5hx6a_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5hx6b_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8072699	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8072699	3000066	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Pkinase_Tyr	e5hx6A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
B	Pkinase_Tyr	e5hx6B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07714	Protein tyrosine and serine/threonine kinase (PK_Tyr_Ser-Thr)	Protein tyrosine and serine/threonine kinase	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosph ...	Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [1]; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Receptor-interacting serine/threonine-protein kinase 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-containing complex binding protein serine/threonine kinase activity JUN kinase kinase kinase activity MAP kinase kinase kinase activity protein binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding death receptor binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity death domain binding protein domain specific binding protein serine kinase activity protein homodimerization activity protein dimerization activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication cellular process response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling regulation of defense response regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response protein-containing complex organization necroptotic process ripoptosome assembly involved in necroptotic process programmed necrotic cell death cell death ripoptosome assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular component organization or biogenesis programmed cell death regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process catabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule catabolic process neuron apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis necroptotic signaling pathway protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process multicellular organismal process positive regulation of interleukin-8 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-8 production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade negative regulation of biological process positive regulation of post-transcriptional gene silencing regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of post-transcriptional gene silencing by RNA RNA processing negative regulation of metabolic process regulation of miRNA processing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing miRNA processing RNA metabolic process regulation of miRNA-mediated gene silencing RNA biosynthetic process nucleic acid biosynthetic process positive regulation of miRNA-mediated gene silencing regulation of regulatory ncRNA processing regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of miRNA processing negative regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity positive regulation of molecular function DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription regulation of localization nitrogen compound transport transport monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of ATP:ADP antiporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity localization regulation of monoatomic anion transport monoatomic anion transmembrane transport monoatomic ion transport nucleobase-containing compound transport regulation of transport regulation of monoatomic ion transport regulation of nucleobase-containing compound transport regulation of monoatomic anion transmembrane transport establishment of localization transmembrane transport regulation of transmembrane transport monoatomic anion transport myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of cell differentiation mononuclear cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation positive regulation of hemopoiesis cell differentiation anatomical structure development regulation of immune system process regulation of macrophage differentiation positive regulation of immune system process developmental process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation positive regulation of cell development macrophage differentiation regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of macrophage differentiation myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation leukocyte differentiation negative regulation of signaling negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway regulation of programmed necrotic cell death positive regulation of programmed necrotic cell death interleukin-6-mediated signaling pathway cellular response to interleukin-6 positive regulation of interleukin-6-mediated signaling pathway response to interleukin-6 regulation of interleukin-6-mediated signaling pathway positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand regulation of extrinsic apoptotic signaling pathway in absence of ligand lymphocyte apoptotic process leukocyte apoptotic process T cell apoptotic process negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction supramolecular fiber organization amyloid fibril formation positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process negative regulation of necroptotic process regulation of necroptotic process negative regulation of programmed necrotic cell death cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification peptidyl-serine autophosphorylation positive regulation of necroptotic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of protein modification process regulation of phosphate metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex endosome membrane membrane-bounded organelle membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex receptor complex endosome membrane membrane-bounded organelle membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle vesicle organelle membrane mitochondrion cell periphery plasma membrane plasma membrane protein complex death-inducing signaling complex membrane protein complex ripoptosome catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR000488	Death domain	Domain
A, B	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR050167	Serine/threonine-protein kinase	Family
A, B	IPR037934	RIP1, Death domain	Domain
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13546	atypical teratoid rhabdoid tumor colorectal adenocarcinoma lupus erythematosus ovarian cancer systemic lupus erythematosus B-cell chronic lymphocytic leukemia glioblastoma malignant ependymoma Philadelphia chromosome-positive acute lymphoblastic leukemia chronic myelogenous leukemia, BCR-ABL1 positive lung cancer malignant glioma pilocytic astrocytoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.