3I8V

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3i8va1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3i8va2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3i8vb1	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	PDEase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3i8vb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	HD-domain/PDEase-like	8067469	3000943	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8067469	3000943	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	PDEase_I	e3i8vA1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)
B	PDEase_I	e3i8vB1	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PDEase_I	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)
B	1.10.1300.10	Mainly Alpha	Orthogonal Bundle	Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00233	3'5'-cyclic nucleotide phosphodiesterase (PDEase_I)	3'5'-cyclic nucleotide phosphodiesterase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	cAMP-specific 3',5'-cyclic phosphodiesterase 4A	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity 3',5'-cyclic-nucleotide phosphodiesterase activity 3',5'-cyclic-AMP phosphodiesterase activity hydrolase activity cyclic-nucleotide phosphodiesterase activity catalytic activity binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 3',5'-cyclic-GMP phosphodiesterase activity cation binding metal ion binding	multicellular organismal process system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cellular process signal transduction multicellular organismal process system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cellular process signal transduction cell communication regulation of signaling regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus regulation of protein kinase A signaling regulation of cell communication protein kinase A signaling adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus cAMP-mediated signaling intracellular signaling cassette ribose phosphate metabolic process ribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process cyclic nucleotide metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleotide catabolic process nucleoside phosphate metabolic process cAMP catabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process cAMP metabolic process cyclic purine nucleotide metabolic process primary metabolic process purine-containing compound catabolic process cyclic nucleotide catabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process metabolic process purine ribonucleotide metabolic process	cellular anatomical structure membrane ruffle cell leading edge plasma membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cellular anatomical structure membrane ruffle cell leading edge plasma membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cytosol extrinsic component of membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036971	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR023174	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Conserved Site
A, B	IPR003607	HD/PDEase domain	Domain
A, B	IPR002073	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Domain
A, B	IPR040844	Phosphodiesterase 4 upstream conserved regions (UCR)	Domain
A, B	IPR023088	3'5'-cyclic nucleotide phosphodiesterase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P27815	psoriasis Chronic Obstructive Pulmonary Disease with Bronchospasms depressive disorder systemic sclerosis Hashimoto thyroiditis inflammatory bowel disease large cell medulloblastoma malignant glioma aphthous stomatitis atopic eczema autism breast fibroadenoma primitive neuroectodermal tumor schizophrenia tuberculosis psoriasis Chronic Obstructive Pulmonary Disease with Bronchospasms depressive disorder systemic sclerosis Hashimoto thyroiditis inflammatory bowel disease large cell medulloblastoma malignant glioma aphthous stomatitis atopic eczema autism breast fibroadenoma primitive neuroectodermal tumor schizophrenia tuberculosis hypothyroidism invasive ductal breast carcinoma lung disease adrenal cortex carcinoma malignant mesothelioma asthma atrial fibrillation osteosarcoma bronchitis chronic obstructive pulmonary disease seasonal affective disorder Crohn disease systemic lupus erythematosus glioblastoma ulcerative colitis juvenile idiopathic arthritis malignant ependymoma ankylosing spondylitis medulloblastoma myositis astrocytic tumor atypical teratoid rhabdoid tumor ovarian cancer bipolar disorder primary biliary cholangitis pulmonary emphysema

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

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.