4MAN | pdb_00004man

Bcl_2-Navitoclax Analog (with Indole) Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d4manb_	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Bcl-2 inhibitors of programmed cell death	Bcl-2 inhibitors of programmed cell death	Bcl-2	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4mana_	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Bcl-2 inhibitors of programmed cell death	Bcl-2 inhibitors of programmed cell death	Bcl-2	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	preSET_CXC	e4manB1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
A	PolyA_pol	e4manA1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: PolyA_pol	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00452	Apoptosis regulator proteins, Bcl-2 family (Bcl-2)	Apoptosis regulator proteins, Bcl-2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Apoptosis regulator Bcl-2	sequence-specific DNA binding DNA binding binding nucleic acid binding death domain binding protein binding BH3 domain binding BH domain binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein phosphatase binding phosphatase binding sequence-specific DNA binding DNA binding binding nucleic acid binding death domain binding protein binding BH3 domain binding BH domain binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein phosphatase binding phosphatase binding protein phosphatase 2A binding protease binding transcription factor binding DNA-binding transcription factor binding molecular adaptor activity identical protein binding protein heterodimerization activity protein dimerization activity passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity molecular function inhibitor activity transporter inhibitor activity channel regulator activity molecular function regulator activity channel inhibitor activity transporter regulator activity	response to stimulus response to chemical response to xenobiotic stimulus inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis response to stimulus response to chemical response to xenobiotic stimulus inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis endoplasmic reticulum calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of biological process regulation of cellular process regulation of mitochondrial depolarization negative regulation of membrane depolarization biological regulation negative regulation of biological process mitochondrial depolarization regulation of membrane depolarization regulation of mitochondrial membrane potential membrane depolarization cellular process regulation of biological quality negative regulation of mitochondrial depolarization regulation of membrane potential response to stress response to ischemia catabolic process autophagy metabolic process process utilizing autophagic mechanism apoptotic process cell death programmed cell death response to radiation response to abiotic stimulus negative regulation of programmed cell death regulation of apoptotic process regulation of anoikis regulation of programmed cell death negative regulation of anoikis negative regulation of apoptotic process anoikis negative regulation of cellular process multicellular organismal process B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis immune system process homeostasis of number of cells lymphocyte homeostasis response to toxic substance developmental process epithelium development epidermis development molting cycle process hair cycle epidermis morphogenesis animal organ development morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis skin development skin epidermis development hair follicle development molting cycle anatomical structure development hair cycle process hair follicle morphogenesis positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of biological process positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process response to metal ion response to iron ion axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis system development plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development mesenchyme development mesenchymal cell development mesenchymal cell differentiation immune system development spleen development hematopoietic or lymphoid organ development negative regulation of locomotion negative regulation of cell motility negative regulation of cell migration carbohydrate derivative biosynthetic process regulation of biosynthetic process regulation of protein metabolic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process macromolecule biosynthetic process regulation of glycoprotein metabolic process regulation of primary metabolic process biosynthetic process regulation of macromolecule biosynthetic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of glycoprotein biosynthetic process ossification digestive system development tube development digestive tract development tube morphogenesis digestive tract morphogenesis negative regulation of catabolic process negative regulation of metabolic process regulation of catabolic process regulation of autophagy negative regulation of autophagy glomerulus development nephron development kidney development renal system development regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process leukocyte apoptotic process negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process T cell apoptotic process negative regulation of lymphocyte apoptotic process regulation of developmental process regulation of cell differentiation positive regulation of cell maturation regulation of neuron maturation regulation of cell development positive regulation of developmental process positive regulation of cell differentiation cell maturation regulation of cell maturation positive regulation of neuron maturation positive regulation of cell development developmental maturation anatomical structure maturation neuron maturation regulation of neuron differentiation organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization response to hydrogen peroxide response to oxidative stress response to oxygen-containing compound response to reactive oxygen species regulation of localization regulation of calcium ion transport cellular localization regulation of calcium ion transport into cytosol transport monoatomic ion transmembrane transport negative regulation of monoatomic ion transport negative regulation of transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport negative regulation of transmembrane transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization negative regulation of monoatomic ion transmembrane transport monoatomic ion transport negative regulation of cation transmembrane transport negative regulation of calcium ion transport into cytosol monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration establishment of localization negative regulation of calcium ion transport transmembrane transport regulation of transmembrane transport regulation of cellular localization regulation of monoatomic cation transmembrane transport negative regulation of calcium ion transmembrane transport negative regulation of cytosolic calcium ion concentration calcium ion transmembrane transport calcium ion transport into cytosol regulation of growth regulation of cellular component organization growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth cochlear nucleus development pons development head development brain development central nervous system development metencephalon development hindbrain development neural nucleus development cell adhesion cell-matrix adhesion regulation of cell-matrix adhesion regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling signaling regulation of signal transduction negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication regulation of apoptotic signaling pathway developmental growth organ growth neuron apoptotic process motor neuron apoptotic process cell population proliferation osteoblast proliferation B cell apoptotic process pigment cell differentiation pigmentation developmental pigmentation melanocyte differentiation sexual reproduction reproductive process multicellular organismal reproductive process oogenesis cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development germ cell development oocyte differentiation response to peptide response to cytokine dendritic cell apoptotic process negative regulation of dendritic cell apoptotic process regulation of dendritic cell apoptotic process positive regulation of cell population proliferation regulation of cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation regulation of cellular response to stress regulation of intrinsic apoptotic signaling pathway in response to DNA damage intracellular signal transduction regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway by p53 class mediator negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator cellular response to stress regulation of intracellular signal transduction regulation of response to stress regulation of signal transduction by p53 class mediator signal transduction by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator DNA damage response regulation of intrinsic apoptotic signaling pathway by p53 class mediator myeloid cell apoptotic process negative regulation of myeloid cell apoptotic process regulation of myeloid cell apoptotic process regulation of protein localization macromolecule localization intracellular protein localization positive regulation of skeletal muscle tissue development muscle cell differentiation regulation of skeletal muscle tissue development myotube differentiation muscle structure development positive regulation of muscle organ development regulation of skeletal muscle fiber development positive regulation of skeletal muscle fiber development muscle tissue development myotube cell development skeletal muscle fiber development positive regulation of striated muscle tissue development regulation of striated muscle tissue development positive regulation of muscle cell differentiation positive regulation of muscle tissue development regulation of muscle cell differentiation positive regulation of multicellular organismal process striated muscle cell differentiation regulation of muscle tissue development skeletal muscle tissue development regulation of striated muscle cell differentiation striated muscle tissue development skeletal muscle organ development striated muscle cell development muscle cell development regulation of myotube differentiation positive regulation of striated muscle cell differentiation regulation of multicellular organismal process muscle organ development regulation of muscle organ development response to ionizing radiation response to gamma radiation stem cell development stem cell differentiation pigment metabolic process phenol-containing compound metabolic process melanin metabolic process secondary metabolic process negative regulation of multicellular organismal process regulation of ossification negative regulation of ossification gonad development reproductive system development sex differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development hemopoiesis B cell lineage commitment mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell fate commitment leukocyte differentiation homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis renal system process system process response to light stimulus response to UV response to UV-B cellular response to nutrient levels response to nutrient levels response to starvation cellular response to glucose starvation cellular response to starvation response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus response to hypoxia response to oxygen levels gene expression regulation of gene expression positive regulation of programmed cell death positive regulation of apoptotic process negative regulation of cell growth negative regulation of growth extrinsic apoptotic signaling pathway via death domain receptors T cell differentiation in thymus T cell activation T cell differentiation protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal female gonad development female sex differentiation development of primary female sexual characteristics ovarian follicle development regulation of protein stability negative regulation of cell population proliferation negative regulation of osteoblast proliferation regulation of osteoblast proliferation mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process metanephros development gland morphogenesis gland development animal organ morphogenesis positive regulation of melanocyte differentiation regulation of pigment cell differentiation regulation of pigmentation positive regulation of developmental pigmentation regulation of melanocyte differentiation positive regulation of pigment cell differentiation regulation of developmental pigmentation sensory organ development visual system development eye morphogenesis regulation of retinal cell programmed cell death sensory system development eye development negative regulation of developmental process programmed cell death involved in cell development sensory organ morphogenesis retinal cell programmed cell death negative regulation of retinal cell programmed cell death focal adhesion assembly cell-substrate junction assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cell-substrate junction organization positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of immune system process positive regulation of immune system process regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of B cell activation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis nephron epithelium development ureteric bud development mesonephros development kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process regulation of B cell apoptotic process negative regulation of B cell apoptotic process immune response-regulating cell surface receptor signaling pathway positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response thymus development vesicle organization cellular pigmentation pigment granule organization ear development multi-multicellular organism process female pregnancy multi-organism reproductive process humoral immune response reactive oxygen species metabolic process T cell homeostasis CD4-positive or CD8-positive, alpha-beta T cell lineage commitment CD8-positive, alpha-beta T cell activation CD8-positive, alpha-beta T cell differentiation alpha-beta T cell differentiation alpha-beta T cell activation alpha-beta T cell lineage commitment T cell lineage commitment CD8-positive, alpha-beta T cell lineage commitment positive T cell selection T cell selection negative regulation of neuron apoptotic process regulation of neuron apoptotic process response to corticosteroid response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation hematopoietic stem cell differentiation regulation of cell cycle phase transition negative regulation of cell cycle regulation of cell cycle G1/S phase transition negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition regulation of cell cycle negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition regulation of G1/S transition of mitotic cell cycle regulation of response to nutrient levels nitrogen utilization regulation of nitrogen utilization intracellular nitrogen homeostasis regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication viral life cycle negative regulation of cellular pH reduction intracellular pH reduction regulation of intracellular pH regulation of cellular pH reduction regulation of pH regulation of cellular pH regeneration response to axon injury neuron projection regeneration axon regeneration response to wounding intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress response to endoplasmic reticulum stress regulation of multicellular organism growth regulation of developmental growth positive regulation of multicellular organism growth multicellular organism growth positive regulation of developmental growth behavioral defense response behavior fear response behavioral fear response multicellular organismal response to stress cell-cell adhesion response to nicotine regulation of membrane permeability regulation of mitochondrial membrane permeability apoptotic mitochondrial changes release of cytochrome c from mitochondria mitochondrion organization intrinsic apoptotic signaling pathway in response to oxidative stress post-embryonic development regulation of motor neuron apoptotic process negative regulation of motor neuron apoptotic process	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein-containing complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein-containing complex BCL-2 complex Bcl-2 family protein complex cytoplasm cytosol pore complex membrane protein complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane mitochondrial membrane mitochondrion organelle outer membrane bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane BAD-BCL-2 complex myelin sheath

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036834	Bcl-2-like superfamily	Homologous Superfamily
A, B	IPR020731	Apoptosis regulator, Bcl-2, BH4 motif, conserved site	Conserved Site
A, B	IPR046371	Bcl-2, Bcl-2 homology region 1-3	Domain
A, B	IPR020717	Apoptosis regulator, Bcl-2, BH1 motif, conserved site	Conserved Site
A, B	IPR004725	Apoptosis regulator, Bcl-2/ BclX	Family
A, B	IPR003093	Apoptosis regulator, Bcl-2 protein, BH4	Domain
A, B	IPR002475	Bcl2-like	Family
A, B	IPR020728	Apoptosis regulator, Bcl-2, BH3 motif, conserved site	Conserved Site
A, B	IPR020726	Apoptosis regulator, Bcl-2, BH2 motif, conserved site	Conserved Site
A, B	IPR013278	Apoptosis regulator, Bcl-2	Family
A, B	IPR026298	Bcl-2 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P10415	B-cell chronic lymphocytic leukemia follicular lymphoma diffuse large B-cell lymphoma acute myeloid leukemia Alzheimer disease synovial sarcoma malignant mesothelioma polycystic ovary syndrome retinal degeneration malignant colon neoplasm plasma cell myeloma mesenchymal chondrosarcoma osteochondrodysplasia male infertility papillary adenoma B-cell chronic lymphocytic leukemia follicular lymphoma diffuse large B-cell lymphoma acute myeloid leukemia Alzheimer disease synovial sarcoma malignant mesothelioma polycystic ovary syndrome retinal degeneration malignant colon neoplasm plasma cell myeloma mesenchymal chondrosarcoma osteochondrodysplasia male infertility papillary adenoma esophageal cancer breast carcinoma type 2 diabetes mellitus Metaplasia clear cell adenocarcinoma alcoholic liver cirrhosis sarcomatoid carcinoma contact dermatitis hypertensive disorder asthma intestinal cancer adenocarcinoma adenoma prostate cancer carcinoma follicular thyroid adenoma microcystic adenoma myocardial infarction granular cell carcinoma allergic contact dermatitis azoospermia erectile dysfunction breast cancer tubular adenocarcinoma cancer gallbladder cancer multiple epiphyseal dysplasia colorectal cancer head and neck cancer neoplasm of neck hematologic disease Schwartz-Jampel syndrome coronary artery disease neurodegenerative disease skin disease depressive disorder inborn carbohydrate metabolic disorder spondyloepiphyseal dysplasia tarda, X-linked ovarian disease intestinal neoplasm ductal breast carcinoma in situ ischemia reperfusion injury bipolar disorder transitional cell carcinoma malignant tumor of neck plasma cell neoplasm maturity-onset diabetes of the young uterine disease prostate carcinoma gallbladder neoplasm psoriasis lymphatic system disease myeloid neoplasm glioblastoma reticulum cell sarcoma colorectal carcinoma neoplasm of esophagus head and neck neoplasm cribriform carcinoma non-alcoholic fatty liver disease osteosarcoma autoimmune disease stomach disease pancreatic intraductal papillary-mucinous carcinoma benign colon neoplasm pituitary cancer kidney disease bipolar I disorder tuberculosis learning disability breast disease undifferentiated carcinoma medulloblastoma fetal alcohol spectrum disorder liver disease prostate disease lung cancer gastric cancer lymphoma colonic neoplasm neoplasm of mature B-cells schizophrenia Sjogren syndrome cribriform carcinoma of breast non-Hodgkin lymphoma idiopathic scoliosis autism spondyloepiphyseal dysplasia lymphosarcoma ovarian cancer intestinal disease pancreatic intraductal papillary-mucinous neoplasm intracerebral hemorrhage benign connective and soft tissue neoplasm toxic encephalopathy large cell medulloblastoma eye disease Melnick-Needles syndrome fetal alcohol syndrome lung disease cerebrovascular disorder gastric carcinoma sarcoidosis connective tissue 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.