Annotations: 7D42

Structural basis of tropifexor as a potent and selective agonist for farnesoid X receptor

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d7d42a_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	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)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8039119	3001442	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		e7d42A1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00104	Ligand-binding domain of nuclear hormone receptor (Hormone_recep)	Ligand-binding domain of nuclear hormone receptor	This all helical domain is involved in binding the hormone in these receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Peptide from Nuclear receptor coactivator 2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding transcription coactivator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development positive regulation of biological process tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process animal gross anatomical part developmental process cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to stimulus response to hormone response to endogenous stimulus response to chemical cellular response to hormone stimulus carboxylic acid transport transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport establishment of localization organic acid transport localization monocarboxylic acid transport macromolecule localization negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular receptor signaling pathway intracellular signal transduction peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm cellular response to nitrogen compound response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex nuclear body
A	Bile acid receptor	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding bile acid binding organic acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding bile acid binding organic acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding small molecule binding transcription factor binding transcription coregulator binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding chenodeoxycholic acid binding steroid binding lipid binding cation binding transition metal ion binding zinc ion binding metal ion binding bile acid nuclear receptor activity	cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response biological regulation defense response to symbiont immune system process cellular process cellular homeostasis chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis intracellular chemical homeostasis intracellular glucose homeostasis multicellular organismal process regulation of tumor necrosis factor production negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process negative regulation of interleukin-2 production regulation of interleukin-2 production interleukin-2 production regulation of low-density lipoprotein particle clearance plasma lipoprotein particle clearance regulation of lipoprotein particle clearance low-density lipoprotein particle clearance regulation of plasma lipoprotein particle levels interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production carboxylic acid transport transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport establishment of localization organic acid transport localization monocarboxylic acid transport macromolecule localization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process defense response to bacterium response to bacterium cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cellular component organization or biogenesis cell-cell junction assembly cell-cell junction organization triglyceride homeostasis acylglycerol homeostasis lipid homeostasis intracellular triglyceride homeostasis 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 regulation of primary metabolic process secondary alcohol metabolic process regulation of small molecule metabolic process small molecule metabolic process lipid metabolic process interleukin-1 production negative regulation of interleukin-1 production regulation of interleukin-1 production cellular response to nitrogen compound positive regulation of cell communication positive regulation of signal transduction response to peptide hormone regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway positive regulation of cellular process cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus regulation of signaling cell surface receptor signaling pathway response to endogenous stimulus regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin regulation of cell communication cellular response to insulin stimulus positive regulation of signaling regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of cellular component organization protein-containing complex remodeling protein-lipid complex organization very-low-density lipoprotein particle remodeling protein-lipid complex remodeling negative regulation of very-low-density lipoprotein particle remodeling plasma lipoprotein particle organization negative regulation of cellular component organization protein-containing complex organization plasma lipoprotein particle remodeling regulation of very-low-density lipoprotein particle remodeling triglyceride-rich lipoprotein particle remodeling glycerophospholipid metabolic process lipid biosynthetic process positive regulation of phosphatidic acid biosynthetic process phospholipid metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process phosphorus metabolic process positive regulation of phosphorus metabolic process phosphatidic acid biosynthetic process glycerophospholipid biosynthetic process phosphatidic acid metabolic process positive regulation of phospholipid biosynthetic process regulation of phospholipid metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process positive regulation of phospholipid metabolic process positive regulation of lipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process regulation of phosphatidic acid biosynthetic process regulation of phosphorus metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process regulation of type II interferon production type II interferon production negative regulation of type II interferon production negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process response to nutrient levels regulation of response to nutrient levels oxoacid metabolic process regulation of nitrogen utilization amino acid metabolic process regulation of ammonia assimilation cycle L-glutamine metabolic process intracellular nitrogen homeostasis glutamate metabolic process regulation of amino acid metabolic process positive regulation of nitrogen utilization nitrogen utilization dicarboxylic acid metabolic process carboxylic acid metabolic process positive regulation of amino acid metabolic process positive regulation of ammonia assimilation cycle proteinogenic amino acid metabolic process ammonia assimilation cycle positive regulation of small molecule metabolic process positive regulation of response to nutrient levels nitrogen cycle metabolic process urea metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process developmental process cellular developmental process cell differentiation regulation of monocyte chemotactic protein-1 production negative regulation of chemokine production monocyte chemotactic protein-1 production negative regulation of monocyte chemotactic protein-1 production regulation of chemokine production chemokine production regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process animal gross anatomical part developmental process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction cellular response to bile acid response to lipid response to bile acid cellular response to lipid negative regulation of inflammatory response regulation of inflammatory response negative regulation of response to external stimulus negative regulation of defense response inflammatory response cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to biotic stimulus response to molecule of bacterial origin sterol homeostasis cholesterol homeostasis regulation of localization establishment of protein localization nitrogen compound transport establishment of localization in cell intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus response to glucose insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion hormone secretion protein localization to extracellular region peptide secretion regulation of secretion by cell secretion by cell response to monosaccharide response to carbohydrate signal release cellular response to hexose stimulus cellular response to monosaccharide stimulus regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling cellular response to glucose stimulus regulation of protein transport peptide transport response to hexose regulation of cellular localization protein transport regulation of insulin secretion peptide hormone secretion regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport insulin secretion positive regulation of establishment of protein localization positive regulation of insulin secretion involved in cellular response to glucose stimulus positive regulation of insulin secretion positive regulation of peptide hormone secretion positive regulation of protein localization positive regulation of secretion by cell positive regulation of protein transport positive regulation of hormone secretion positive regulation of secretion positive regulation of peptide secretion positive regulation of protein secretion positive regulation of transport fatty acid homeostasis interleukin-17 production regulation of interleukin-17 production positive regulation of gene expression positive regulation of interleukin-17 production positive regulation of cytokine production regulation of steroid biosynthetic process ketone metabolic process carboxylic acid biosynthetic process steroid biosynthetic process bile acid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process regulation of bile acid biosynthetic process regulation of ketone metabolic process bile acid metabolic process monocarboxylic acid metabolic process response to fatty acid cellular response to fatty acid bile acid signaling pathway nuclear receptor-mediated bile acid signaling pathway nuclear receptor-mediated signaling pathway response to cytokine cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway response to tumor necrosis factor	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen chromatin chromosome protein-containing complex signaling receptor complex RNA polymerase II transcription regulator complex nuclear protein-containing complex transcription regulator complex euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
B	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
B	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
B	IPR017426	Nuclear receptor coactivator	Family
B	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
B	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
B	IPR013767	PAS fold	Domain
B	IPR000014	PAS domain	Domain
B	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
B	IPR035965	PAS domain superfamily	Homologous Superfamily
B	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
B	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
B	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A	IPR001728	Thyroid hormone receptor	Family
A	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A	IPR044114	Bile acid receptor, ligand binding domain	Domain
A	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A	IPR001723	Nuclear hormone receptor	Family
A	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	: Q15596	breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm testicular germ cell tumor breast cancer endogenous depression glioblastoma medulloblastoma plasma cell myeloma
A	: Q96RI1	Crohn disease cholestasis non-alcoholic fatty liver disease cholestasis, progressive familial intrahepatic, 5 Extravasation of Diagnostic and Therapeutic Materials intestinal cancer intrahepatic cholestasis liver disease liver cancer fatty liver disease hepatocellular carcinoma inborn carbohydrate metabolic disorder adenoma cirrhosis of liver male infertility Crohn disease cholestasis non-alcoholic fatty liver disease cholestasis, progressive familial intrahepatic, 5 Extravasation of Diagnostic and Therapeutic Materials intestinal cancer intrahepatic cholestasis liver disease liver cancer fatty liver disease hepatocellular carcinoma inborn carbohydrate metabolic disorder adenoma cirrhosis of liver male infertility obesity disorder drug-induced liver injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive familial intrahepatic cholestasis type 1 transitional cell carcinoma intestinal neoplasm malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma primary biliary cholangitis type 2 diabetes mellitus ileocolitis interstitial cystitis liver neoplasm Crohn's colitis nephrosclerosis pancreatic intraductal papillary-mucinous carcinoma