3QU8

Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-(4-Nitrobenzyl)pyridine.

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)
C	d3qu8c1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qu8c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3qu8d_	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3qu8f_	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qu8a1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qu8a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qu8b1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qu8b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3qu8e1	All alpha proteins	Cytochrome P450	Cytochrome P450	Cytochrome P450	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3qu8e2	Artifacts	Tags	Tags	Tags	C-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)
C	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytochrome P450	8068635	3001061	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)
C	p450	e3qu8C1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
D	p450	e3qu8D1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
F	p450	e3qu8F1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
A	p450	e3qu8A1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
B	p450	e3qu8B1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)
E	p450	e3qu8E1	A: alpha arrays	X: Cytochrome P450 (From Topology)	H: Cytochrome P450 (From Topology)	T: Cytochrome P450	F: p450	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
D	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
F	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
A	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
B	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)
E	1.10.630.10	Mainly Alpha	Orthogonal Bundle	Cytochrome p450	Cytochrome P450	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00067	Cytochrome P450 (p450)	Cytochrome P450	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, a ...	Cytochrome P450s are haem-thiolate proteins [6] involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Cytochrome P450 2B6	oxidoreductase activity monooxygenase activity anandamide 8,9 epoxidase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity anandamide epoxidase activity arachidonate monooxygenase activity arachidonate epoxygenase activity anandamide 11,12 epoxidase activity estrogen 2-hydroxylase activity steroid hydroxylase activity testosterone 16-beta-hydroxylase activity anandamide 14,15 epoxidase activity oxidoreductase activity monooxygenase activity anandamide 8,9 epoxidase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity anandamide epoxidase activity arachidonate monooxygenase activity arachidonate epoxygenase activity anandamide 11,12 epoxidase activity estrogen 2-hydroxylase activity steroid hydroxylase activity testosterone 16-beta-hydroxylase activity anandamide 14,15 epoxidase activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding testosterone 16-alpha-hydroxylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	icosanoid metabolic process fatty acid metabolic process long-chain fatty acid metabolic process unsaturated fatty acid metabolic process epoxygenase P450 pathway oxoacid metabolic process arachidonate metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process olefinic compound metabolic process metabolic process cellular process small molecule metabolic process icosanoid metabolic process fatty acid metabolic process long-chain fatty acid metabolic process unsaturated fatty acid metabolic process epoxygenase P450 pathway oxoacid metabolic process arachidonate metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process olefinic compound metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process steroid metabolic process cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus catabolic process xenobiotic catabolic process ketone metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle intracellular membrane-bounded organelle cytoplasm organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002401	Cytochrome P450, E-class, group I	Family
A, B, C, D, E A, B, C, D, E, F	IPR017972	Cytochrome P450, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR008068	Cytochrome P450, E-class, group I, CYP2B-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR050182	Cytochrome P450 family 2	Family
A, B, C, D, E A, B, C, D, E, F	IPR001128	Cytochrome P450	Family
A, B, C, D, E A, B, C, D, E, F	IPR036396	Cytochrome P450 superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P20813	gliosarcoma chronic kidney disease efavirenz, poor metabolism of Nonorganic psychosis paranoid schizophrenia sinusitis lung adenocarcinoma nephrosclerosis opiate dependence psoriasis Sjogren syndrome ulcerative colitis lung cancer nicotine dependence pancreatic ductal adenocarcinoma gliosarcoma chronic kidney disease efavirenz, poor metabolism of Nonorganic psychosis paranoid schizophrenia sinusitis lung adenocarcinoma nephrosclerosis opiate dependence psoriasis Sjogren syndrome ulcerative colitis lung cancer nicotine dependence pancreatic ductal adenocarcinoma peripheral arterial disease chronic obstructive pulmonary disease drug-induced liver injury hepatocellular carcinoma lung 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.