7ND1 | pdb_00007nd1

First-in-class small molecule inhibitors of Polycomb Repressive Complex 1 (PRC1) RING domain

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth H]	SCOP2B Superfamily	RING/U-box like	8079705	3000160	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 [auth H]	TFIIA_gamma_C	e7nd1H1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: TFIIA_gamma_C	ECOD (develop294)
A	TFIIA_gamma_C	e7nd1A1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: TFIIA_gamma_C	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	PF13923	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)	Zinc finger, C3HC4 type (RING finger)		Domain
A	PF13923	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)	Zinc finger, C3HC4 type (RING finger)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	Polycomb complex protein BMI-1	enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding cation binding transition metal ion binding enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding promoter-specific chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification head development central nervous system development animal organ development brain development nervous system development system development developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification head development central nervous system development animal organ development brain development nervous system development system development humoral immune response response to stimulus immune response immune system process regulation of cellular process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal fibroblast proliferation cell population proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process cellular developmental process hemopoiesis cell differentiation cell development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development anatomical structure morphogenesis embryo development ending in birth or egg hatching skeletal system development animal organ morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis cellular response to stimulus response to ketone response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone negative regulation of biological process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic in utero embryonic development cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of signaling signaling regulation of signal transduction regulation of programmed cell death negative regulation of cell communication cell communication negative regulation of apoptotic signaling pathway signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway epithelium development neural tube development tube development anterior/posterior pattern specification tissue development rostrocaudal neural tube patterning neural tube patterning positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of immune system process regulation of multicellular organismal process positive regulation of immune system process regulation of lymphocyte proliferation regulation of leukocyte proliferation B cell activation cell activation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation regulation of developmental process regulation of kidney development renal system development kidney development somatic stem cell division stem cell division cell division RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of adaxial/abaxial pattern formation adaxial/abaxial pattern specification mononuclear cell differentiation lymphocyte differentiation T cell differentiation in thymus T cell activation regulation of immature T cell proliferation T cell differentiation positive regulation of T cell activation positive regulation of immature T cell proliferation regulation of immature T cell proliferation in thymus positive regulation of T cell proliferation regulation of leukocyte cell-cell adhesion leukocyte differentiation immature T cell proliferation in thymus positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of immature T cell proliferation in thymus T cell proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation immature T cell proliferation regulation of T cell proliferation response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex cytoplasm cytosol PRC1 complex ubiquitin ligase complex membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex cytoplasm cytosol PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin nuclear body
A	E3 ubiquitin-protein ligase RING2	protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity protein binding binding RING-like zinc finger domain binding protein domain specific binding chromatin binding aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity histone modifying activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular process cell cycle mitotic cell cycle developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation sexual reproduction cellular developmental process cellular process cell cycle mitotic cell cycle developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation germ cell development regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal anterior/posterior axis specification anterior/posterior pattern specification pattern specification process axis specification regionalization negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule 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 metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex sex chromosome intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex sex chromosome intracellular membraneless organelle chromatin chromosome heterochromatin sex chromatin membraneless organelle PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen euchromatin nuclear body histone methyltransferase complex MLL1/2 complex MLL1 complex methyltransferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B [auth H]	IPR032443	RAWUL domain	Domain
B [auth H]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth H]	IPR001841	Zinc finger, RING-type	Domain
A	IPR043540	E3 ubiquitin-protein ligase RING1/RING2	Family
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR032443	RAWUL domain	Domain
A	IPR037937	E3 ubiquitin-protein ligase RING2, RAWUL domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth H]	Pharos: P35226	glioblastoma osteosarcoma malignant glioma leukemia, myeloid, accelerated-phase mixed glioma cancer myelodysplastic syndrome giant cell glioblastoma breast carcinoma Disease Exacerbation glioma ovarian cancer dermatomyositis medulloblastoma
A	Pharos: Q99496	astrocytic tumor oligodendroglioma breast carcinoma epilepsy

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.