5XQX | pdb_00005xqx

Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079143	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)
B	Nrd1-Seb1_dom2	e5xqxB1	A: alpha bundles	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (develop294)
A	Nrd1-Seb1_dom2	e5xqxA1	A: alpha bundles	X: CRISPR-associated protein Cse2	H: CRISPR-associated protein Cse2	T: CRISPR-associated protein Cse2	F: Nrd1-Seb1_dom2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF16899	Cyclin C-terminal domain (Cyclin_C_2)	Cyclin C-terminal domain	Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H [1].	Domain
B	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Cyclin-C	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity identical protein binding protein binding binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process G0 to G1 transition cell cycle cell cycle process cellular response to stimulus response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of cellular process signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction Notch signaling pathway negative regulation of Notch signaling pathway regulation of response to stimulus regulation of Notch signaling pathway regulation of cell communication	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex mediator complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A	Cyclin-dependent kinase 8	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity cyclin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity protein serine kinase activity	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen mediator complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR031658	Cyclin, C-terminal domain 2	Domain
B	IPR006671	Cyclin, N-terminal	Domain
B	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B	IPR013763	Cyclin-like domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P24863	IgA glomerulonephritis ovarian cancer juvenile dermatomyositis pancreatic ductal adenocarcinoma myopathy spina bifida
A	Pharos: P49336	adrenal cortex carcinoma colorectal adenocarcinoma lung cancer ovarian cancer pituitary cancer subependymal giant cell astrocytoma breast cancer intellectual disability medulloblastoma pancreatic intraductal papillary-mucinous neoplasm pituitary gland adenoma chronic myelogenous leukemia, BCR-ABL1 positive large cell medulloblastoma osteosarcoma Philadelphia chromosome-positive acute lymphoblastic leukemia adrenal cortex carcinoma colorectal adenocarcinoma lung cancer ovarian cancer pituitary cancer subependymal giant cell astrocytoma breast cancer intellectual disability medulloblastoma pancreatic intraductal papillary-mucinous neoplasm pituitary gland adenoma chronic myelogenous leukemia, BCR-ABL1 positive large cell medulloblastoma osteosarcoma Philadelphia chromosome-positive acute lymphoblastic leukemia psoriasis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.