9JK1 | pdb_00009jk1

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth C]	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062460	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062460	3000066	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth C]	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
B [auth D], D [auth C]	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain
A, C [auth B]	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 [auth D], D [auth C]	Cyclin-K	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 protein binding binding kinase binding enzyme 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 protein binding binding kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity cyclin-dependent protein kinase regulator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process host-mediated suppression of viral genome replication biological process involved in interspecies interaction between organisms viral genome replication viral process viral life cycle host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process host-mediated suppression of viral genome replication biological process involved in interspecies interaction between organisms viral genome replication viral process viral life cycle host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont 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 positive regulation of DNA-templated transcription, elongation 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 DNA-templated transcription elongation regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cell division regulation of signaling signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction transcription by RNA polymerase II transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm cyclin/CDK positive transcription elongation factor complex intracellular membrane-bounded organelle organelle lumen carboxy-terminal domain protein kinase complex organelle nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen cyclin K-CDK13 complex
A, C [auth B]	Cyclin-dependent kinase 12	protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 cyclin-dependent protein kinase activity kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process cellular process negative regulation of cell differentiation RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process mRNA processing mRNA metabolic process RNA processing RNA splicing cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of MAP kinase activity regulation of primary metabolic process phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus estrogen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway response to estrogen cellular response to estrogen stimulus transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation 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 DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen transcription elongation factor complex nuclear protein-containing complex cyclin/CDK positive transcription elongation factor complex carboxy-terminal domain protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth C]	IPR004367	Cyclin, C-terminal domain	Domain
B [auth D], D [auth C]	IPR006671	Cyclin, N-terminal	Domain
B [auth D], D [auth C]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B [auth D], D [auth C]	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B [auth D], D [auth C]	IPR013763	Cyclin-like domain	Domain
A, C [auth B]	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C [auth B]	IPR000719	Protein kinase domain	Domain
A, C [auth B]	IPR050108	Cyclin-dependent kinase	Family
A, C [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C [auth B]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D], D [auth C]	Pharos: O75909	malignant pancreatic neoplasm pancreatic ductal adenocarcinoma osteosarcoma psoriasis ovarian cancer
A, C [auth B]	Pharos: Q9NYV4	prostate cancer rheumatoid arthritis colorectal adenocarcinoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor psoriasis large cell medulloblastoma Neoplasm of uncertain or unknown behavior of ovary ovarian carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia osteosarcoma ovarian neoplasm Pick disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C [auth B]	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.