3PDC | pdb_00003pdc

Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor

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)
B	d3pdcb_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3pdca_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	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)
B	SCOP2B Superfamily	alpha/beta-Hydrolases	8035616	3000102	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha/beta-Hydrolases	8035616	3000102	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	Globin	e3pdcB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (develop294)
A	Globin	e3pdcA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00561	alpha/beta hydrolase fold (Abhydrolase_1)	alpha/beta hydrolase fold	This catalytic domain is found in a very wide range of enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Epoxide hydrolase 2	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds lipid phosphatase activity phosphatase activity hydrolase activity catalytic activity binding toxic substance binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds lipid phosphatase activity phosphatase activity hydrolase activity catalytic activity binding toxic substance binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity lysophosphatidic acid phosphatase activity epoxide hydrolase activity ether hydrolase activity hydrolase activity, acting on ether bonds 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity	stilbene catabolic process catabolic process benzene-containing compound metabolic process olefinic compound catabolic process metabolic process cellular process olefinic compound metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression stilbene catabolic process catabolic process benzene-containing compound metabolic process olefinic compound catabolic process metabolic process cellular process olefinic compound metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological 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 positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process regulation of growth regulation of cellular component organization growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis epoxide metabolic process response to stimulus response to chemical response to toxic substance regulation of cholesterol metabolic process sterol metabolic process steroid metabolic process regulation of steroid metabolic process regulation of lipid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process regulation of primary metabolic process secondary alcohol metabolic process regulation of small molecule metabolic process small molecule metabolic process lipid metabolic process dephosphorylation phosphate-containing compound metabolic process phosphorus metabolic process phospholipid dephosphorylation lipid modification	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle peroxisome microbody intracellular membrane-bounded organelle peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000639	Epoxide hydrolase-like	Family
A, B	IPR011945	Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal	Domain
A, B	IPR006439	HAD hydrolase, subfamily IA	Family
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR000073	Alpha/beta hydrolase fold-1	Domain
A, B	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR023198	Phosphoglycolate phosphatase-like, domain 2	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P34913	familial hypercholesterolemia Ventricular Dysfunction, Left congestive heart failure autism spectrum disorder staphyloenterotoxemia ulcerative colitis hepatocellular carcinoma acute kidney failure lung carcinoma adrenal cortex carcinoma malignant pancreatic neoplasm Alzheimer disease attention deficit hyperactivity disorder, inattentive type ovarian cancer bipolar disorder familial hypercholesterolemia Ventricular Dysfunction, Left congestive heart failure autism spectrum disorder staphyloenterotoxemia ulcerative colitis hepatocellular carcinoma acute kidney failure lung carcinoma adrenal cortex carcinoma malignant pancreatic neoplasm Alzheimer disease attention deficit hyperactivity disorder, inattentive type ovarian cancer bipolar disorder pancreatic intraductal papillary-mucinous neoplasm sarcoidosis cutaneous lupus erythematosus toxic shock syndrome heart failure interstitial cystitis malignant colon neoplasm anorexia nervosa atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma breast cancer psoriasis schizophrenia tuberculosis gastrointestinal stromal tumor hypercholesterolemia, familial, 1 intrinsic asthma malignant ependymoma allergic asthma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma cannabis dependence renal cell carcinoma coronary artery disease

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.