3WKB

Crystal structure of soluble epoxide hydrolase in complex with fragment 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)
A	d3wkba2	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Epoxide hydrolase	Mammalian epoxide hydrolase, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3wkba1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	YihX-like	Epoxide hydrolase, N-terminal domain	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	alpha/beta-Hydrolases	8035616	3000102	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8035613	3001890	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	HAD_2	e3wkbA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: HAD_2	ECOD (1.6)
A	Hydrolase_4_2	e3wkbA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	1.10.150.240	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	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	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	Domain
A	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	Bifunctional 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 olefinic compound metabolic process metabolic process cellular process stilbene 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 stilbene catabolic process catabolic process benzene-containing compound metabolic process olefinic compound catabolic process olefinic compound metabolic process metabolic process cellular process stilbene 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 sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis ether metabolic process epoxide metabolic process small molecule metabolic process response to stimulus response to chemical response to toxic substance regulation of cholesterol metabolic process organic hydroxy compound 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 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	IPR000639	Epoxide hydrolase-like	Family
A	IPR011945	Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal	Domain
A	IPR006439	HAD hydrolase, subfamily IA	Family
A	IPR023214	HAD superfamily	Homologous Superfamily
A	IPR000073	Alpha/beta hydrolase fold-1	Domain
A	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A	IPR036412	HAD-like superfamily	Homologous Superfamily
A	IPR023198	Phosphoglycolate phosphatase-like, domain 2	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

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

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.