Annotations: 8CIE

Crystal structure of the human CDKL5 kinase domain with compound YL-354

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)	8069159	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	MRS2-like	e8cieA1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: MRS2-like	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A	Cyclin-dependent kinase-like 5	small GTPase binding protein binding binding enzyme binding GTPase binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding small GTPase binding protein binding binding enzyme binding GTPase binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor 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	cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling Rac protein signal transduction biological regulation positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization axon extension positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth regulation of cell differentiation regulation of neurogenesis regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron projection morphogenesis positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth positive regulation of cell development developmental growth involved in morphogenesis positive regulation of multicellular organismal process positive regulation of cellular component organization plasma membrane bounded cell projection morphogenesis cell growth cell morphogenesis regulation of axon extension regulation of nervous system development regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth anatomical structure morphogenesis regulation of anatomical structure size trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization organelle assembly regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly organelle organization regulation of organelle assembly cell projection assembly neuron migration cell migration cell motility postsynapse organization regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of cell morphogenesis regulation of dendrite morphogenesis positive regulation of cell morphogenesis positive regulation of dendrite morphogenesis dendrite morphogenesis	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton dendrite terminus axon neuron projection plasma membrane bounded cell projection intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton dendrite terminus axon neuron projection plasma membrane bounded cell projection growth cone somatodendritic compartment cell projection distal axon dendritic growth cone dendrite dendritic tree site of polarized growth membrane-bounded organelle ciliary tip cilium nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse cell junction glutamatergic synapse neuron projection cytoplasm dendrite cytoplasm cytoplasm ciliary basal body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: O76039	developmental and epileptic encephalopathy, 2 Rett syndrome Angelman syndrome West syndrome intellectual disability epilepsy visual epilepsy atypical Rett syndrome Generalized Absence Seizures malignant ependymoma metastatic melanoma astrocytic tumor atypical teratoid rhabdoid tumor ovarian cancer developmental and epileptic encephalopathy developmental and epileptic encephalopathy, 2 Rett syndrome Angelman syndrome West syndrome intellectual disability epilepsy visual epilepsy atypical Rett syndrome Generalized Absence Seizures malignant ependymoma metastatic melanoma astrocytic tumor atypical teratoid rhabdoid tumor ovarian cancer developmental and epileptic encephalopathy pituitary cancer large cell medulloblastoma X-linked retinoschisis malignant glioma adrenal cortex carcinoma microcephaly colorectal cancer oligodendroglioma ovarian serous adenocarcinoma developmental and epileptic encephalopathy, 1 primitive neuroectodermal tumor glioblastoma interstitial cystitis lung adenocarcinoma medulloblastoma osteosarcoma Crohn disease pilocytic astrocytoma

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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.