Annotations: 43NO

Crystal structure of a de novo-designed Binder targeting VEGFA

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D, G, H	PF00341	PDGF/VEGF domain (PDGF)	PDGF/VEGF domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, G, H	Vascular endothelial growth factor A, long form	protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity molecular function activator activity protein kinase regulator activity signaling receptor activator activity protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding vascular endothelial growth factor receptor 1 binding cytokine receptor binding vascular endothelial growth factor receptor binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity molecular function activator activity protein kinase regulator activity signaling receptor activator activity kinase activator activity enzyme activator activity molecular function regulator activity signaling receptor regulator activity protein kinase activator activity kinase regulator activity neuropilin binding vascular endothelial growth factor receptor 2 binding growth factor activity receptor ligand activity fibronectin binding identical protein binding extracellular matrix binding cytokine activity chemoattractant activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	regulation of biological process regulation of cellular process regulation of cell adhesion biological regulation negative regulation of biological process negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion mediated by cadherin cell-cell adhesion mediated by cadherin negative regulation of cell-cell adhesion negative regulation of cellular process regulation of cell-cell adhesion cellular process regulation of biological process regulation of cellular process regulation of cell adhesion biological regulation negative regulation of biological process negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion mediated by cadherin cell-cell adhesion mediated by cadherin negative regulation of cell-cell adhesion negative regulation of cellular process regulation of cell-cell adhesion cellular process regulation of cell-cell adhesion mediated by cadherin multicellular organismal process multicellular organismal-level homeostasis chemical homeostasis homeostatic process multicellular organismal-level chemical homeostasis surfactant homeostasis cellular response to stimulus cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus signal transduction response to growth factor enzyme-linked receptor protein signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus regulation of vascular endothelial growth factor signaling pathway positive regulation of cellular process regulation of signaling regulation of cellular response to vascular endothelial growth factor stimulus regulation of cellular response to growth factor stimulus positive regulation of vascular endothelial growth factor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling positive regulation of locomotion regulation of cell motility regulation of response to external stimulus positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to external stimulus taxis positive regulation of cell motility regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process cell motility positive regulation of immune system process locomotion regulation of mast cell chemotaxis cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration mast cell migration response to external stimulus positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration regulation of chemotaxis leukocyte migration positive regulation of mast cell chemotaxis cellular response to chemical stimulus immune system process regulation of locomotion response to chemical mast cell chemotaxis leukocyte chemotaxis developmental process blood vessel morphogenesis tube development artery development vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development artery morphogenesis animal gross anatomical part developmental process blood vessel development system development regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization cellular component organization cellular component biogenesis cellular component assembly cell junction assembly positive regulation of cell-substrate adhesion regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis regulation of cell-substrate adhesion positive regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication intracellular signal transduction nitric oxide-cGMP-mediated signaling regulation of intracellular signal transduction intracellular signaling cassette negative regulation of nitric oxide-cGMP mediated signal transduction negative regulation of response to stimulus regulation of nitric oxide-cGMP mediated signal transduction negative regulation of signal transduction branching morphogenesis of an epithelial tube angiogenesis epithelial tube morphogenesis epithelium development morphogenesis of an epithelium tissue development branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure anatomical structure formation involved in morphogenesis morphogenesis of a branching epithelium nervous system development phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process regulation of cell differentiation mesenchyme development cell differentiation negative regulation of cell differentiation regulation of multicellular organismal process negative regulation of developmental process animal organ development negative regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition mesenchymal cell differentiation negative regulation of multicellular organismal process regulation of vascular permeability system process circulatory system process positive regulation of vascular permeability vascular process in circulatory system regulation of biological quality blood circulation regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation smooth muscle cell differentiation cardiac vascular smooth muscle cell development cell development muscle cell differentiation muscle structure development vascular associated smooth muscle cell differentiation muscle cell development vascular associated smooth muscle cell development cardiac cell development heart development cardiac vascular smooth muscle cell differentiation coronary vasculature development cardiocyte differentiation 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 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 biosynthetic 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive chemotaxis positive regulation of positive chemotaxis induction of positive chemotaxis regulation of positive chemotaxis positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade mesonephric epithelium development kidney epithelium development nephron tubule morphogenesis regulation of kidney development regulation of branching involved in ureteric bud morphogenesis positive regulation of developmental process animal organ morphogenesis nephron development regulation of morphogenesis of a branching structure regulation of animal organ morphogenesis positive regulation of multicellular organismal process mesonephric tubule development renal tubule morphogenesis nephron morphogenesis nephron epithelium morphogenesis nephron tubule development renal system development ureteric bud morphogenesis positive regulation of morphogenesis of an epithelium branching involved in ureteric bud morphogenesis renal tubule development regulation of morphogenesis of an epithelium regulation of anatomical structure morphogenesis nephron epithelium development ureteric bud development mesonephros development kidney morphogenesis positive regulation of branching involved in ureteric bud morphogenesis mesonephric tubule morphogenesis kidney development 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 axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development retinal ganglion cell axon guidance axon extension positive regulation of nervous system development regulation of growth regulation of cellular component size developmental growth regulation of neurogenesis regulation of cell development positive regulation of axon extension involved in axon guidance positive regulation of cell projection organization positive regulation of developmental growth regulation of cell projection organization positive regulation of cell development developmental growth involved in morphogenesis regulation of neuron projection development cell growth regulation of axon extension regulation of nervous system development regulation of axon extension involved in axon guidance regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis axon extension involved in axon guidance positive regulation of axon extension positive regulation of axonogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth developmental cell growth growth positive regulation of cell growth regulation of cell growth positive regulation of growth regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size neuron migration motor neuron migration sensory organ development photoreceptor cell differentiation visual system development eye morphogenesis eye photoreceptor cell differentiation sensory system development photoreceptor cell development eye photoreceptor cell development eye development sensory organ morphogenesis positive regulation of epithelial tube formation tube formation epithelial tube formation regulation of epithelial tube formation anatomical structure maturation cell maturation developmental maturation cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of miRNA transcription miRNA transcription regulation of miRNA metabolic process miRNA metabolic process negative regulation of miRNA metabolic process regulation of miRNA transcription basophil chemotaxis granulocyte migration granulocyte chemotaxis regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration blood vessel endothelial cell migration regulation of endothelial cell migration lymph vessel morphogenesis lymph vessel development regulation of vasculature development positive regulation of angiogenesis regulation of blood vessel branching positive regulation of blood vessel branching positive regulation of vasculature development regulation of angiogenesis myeloid leukocyte differentiation hemopoiesis macrophage differentiation mononuclear cell differentiation myeloid cell differentiation leukocyte differentiation vasculogenesis cardiac muscle cell development striated muscle tissue development striated muscle cell development muscle tissue development cardiac muscle tissue development cardiac muscle cell differentiation striated muscle cell differentiation regulation of sprouting angiogenesis positive regulation of sprouting angiogenesis sprouting angiogenesis wound healing angiogenesis involved in wound healing vascular wound healing response to stress response to wounding negative regulation of gene expression endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation vascular endothelial growth factor receptor signaling pathway dopaminergic neuron differentiation mammary gland lobule development mammary gland alveolus development positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation protein autophosphorylation phosphorylation regulation of protein metabolic process regulation of protein autophosphorylation macromolecule modification regulation of phosphorylation positive regulation of protein autophosphorylation heart morphogenesis outflow tract morphogenesis post-embryonic camera-type eye development camera-type eye development post-embryonic development regulation of establishment of endothelial barrier endothelium development negative regulation of endothelial cell development epithelial cell differentiation regulation of epithelial cell differentiation endothelial cell development regulation of endothelial cell development negative regulation of epithelial cell differentiation endothelial cell differentiation regulation of endothelial cell differentiation negative regulation of endothelial cell differentiation negative regulation of cell development epithelial cell development establishment of endothelial barrier negative regulation of establishment of endothelial barrier mesoderm development regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis blood vessel endothelial cell proliferation involved in sprouting angiogenesis primitive hemopoiesis embryo development myeloid cell homeostasis embryonic organ development erythrocyte homeostasis erythrocyte differentiation embryonic hemopoiesis primitive erythrocyte differentiation homeostasis of number of cells positive regulation of macromolecule biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to oxygen levels response to abiotic stimulus protein-containing complex organization positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway VEGF-activated platelet-derived growth factor receptor signaling pathway platelet-derived growth factor receptor signaling pathway cell migration involved in sprouting angiogenesis embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development gonad development reproductive system development reproductive process female gonad development sex differentiation female sex differentiation development of primary female sexual characteristics developmental process involved in reproduction development of primary sexual characteristics reproductive structure development ovarian follicle development vascular endothelial growth factor receptor-2 signaling pathway camera-type eye morphogenesis monocyte differentiation multi-multicellular organism process regulation of trophoblast cell migration regulation of reproductive process ameboidal-type cell migration female pregnancy embryo implantation positive regulation of reproductive process trophoblast cell migration positive regulation of trophoblast cell migration multi-organism reproductive process positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cell migration involved in sprouting angiogenesis regulation of cell migration involved in sprouting angiogenesis cellular response to acid chemical stress response to acid chemical response to acid chemical cellular stress response to acid chemical endothelial cell chemotaxis regulation of localization import into cell receptor internalization regulation of receptor internalization vesicle-mediated transport positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis respiratory tube development lung development respiratory system development neuropilin signaling pathway VEGF-activated neuropilin signaling pathway regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction commissural neuron axon guidance positive regulation of protein localization to early endosome regulation of protein localization protein localization to endosome protein localization to early endosome regulation of protein localization to endosome macromolecule localization protein localization to organelle positive regulation of protein localization intracellular protein localization positive regulation of protein localization to endosome regulation of protein localization to early endosome coronary artery morphogenesis coronary vasculature morphogenesis regulation of cell shape regulation of cell morphogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of endothelial cell chemotaxis regulation of endothelial cell chemotaxis regulation of blood-brain barrier permeability maintenance of blood-brain barrier tissue homeostasis negative regulation of vascular permeability anatomical structure homeostasis negative regulation of blood-brain barrier permeability adherens junction organization negative regulation of cellular component organization negative regulation of adherens junction organization regulation of adherens junction organization cell-cell junction organization regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process DNA metabolic process positive regulation of DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process venous blood vessel development venous blood vessel morphogenesis coronary vein morphogenesis neuroblast proliferation regulation of neuroblast proliferation regulation of neural precursor cell proliferation positive regulation of neural precursor cell proliferation positive regulation of neuroblast proliferation neural precursor cell proliferation positive regulation of cell migration by vascular endothelial growth factor signaling pathway positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway	cell surface cellular anatomical structure extracellular matrix external encapsulating structure extracellular region membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cell surface cellular anatomical structure extracellular matrix external encapsulating structure extracellular region membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle cell-cell junction adherens junction anchoring junction cell junction Golgi apparatus vesicle lumen membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen organelle lumen platelet alpha granule platelet alpha granule lumen protein-containing complex VEGF-A complex growth factor complex nucleus endoplasmic reticulum
A, B, E, F	VEGFA_Binder-004	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, G, H	IPR029034	Cystine-knot cytokine	Homologous Superfamily
C, D, G, H	IPR036841	Vascular endothelial growth factor, heparin-binding domain superfamily	Homologous Superfamily
C, D, G, H	IPR023581	Platelet-derived growth factor, conserved site	Conserved Site
C, D, G, H	IPR000072	PDGF/VEGF domain	Domain
C, D, G, H	IPR027928	Vascular endothelial growth factor, heparin-binding domain	Domain
C, D, G, H	IPR050507	Platelet-derived/Vascular endothelial growth factor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D, G, H	: P15692	age-related macular degeneration glioblastoma diabetic retinopathy heart disease retinal vein occlusion psoriasis osteosarcoma squamous cell carcinoma atherosclerosis rheumatoid arthritis angiosarcoma myeloid leukemia portal hypertension macular retinal edema status epilepticus age-related macular degeneration glioblastoma diabetic retinopathy heart disease retinal vein occlusion psoriasis osteosarcoma squamous cell carcinoma atherosclerosis rheumatoid arthritis angiosarcoma myeloid leukemia portal hypertension macular retinal edema status epilepticus coronary artery disease gliosarcoma cancer pancreatic ductal adenocarcinoma rhabdomyosarcoma Alzheimer disease wet macular degeneration multiple epiphyseal dysplasia Arthritis, Experimental malignant colon neoplasm cirrhosis of liver prostate cancer proteinuria contact dermatitis gastric ulcer osteochondrodysplasia cystoid macular edema granular cell carcinoma lung disease asthma cervical cancer hepatocellular carcinoma tubular adenocarcinoma adenocarcinoma retinal disease retinopathy of prematurity giant cell glioblastoma breast cancer head and neck cancer liver failure chronic monocytic leukemia endometrial carcinoma temporal lobe epilepsy thrombotic microangiopathy erectile dysfunction type 2 diabetes mellitus congestive heart failure non-small cell lung carcinoma corneal neovascularization microvascular complications of diabetes, susceptibility to, 1 arthritic joint disease head and neck neoplasm polycystic ovary syndrome lung adenocarcinoma diabetic macular edema myocardial ischemia cerebrovascular disorder precancerous condition lymphatic system disease hemangioma stomach disease benign colon neoplasm hypertensive disorder malignant glioma malignant pancreatic neoplasm benign urinary system neoplasm neovascular glaucoma MALT lymphoma tuberculosis bone marrow disease neurodegenerative disease pustulosis palmaris et plantaris exocrine pancreatic carcinoma ulcerative colitis non-alcoholic fatty liver disease intracerebral hemorrhage retinal detachment kidney disease metabolic syndrome X learning disability cribriform carcinoma of breast bronchitis ovarian disease dermatomyositis skin disease liver disease spinal cord injury spondyloepiphyseal dysplasia heart failure drug-induced liver injury atypical teratoid rhabdoid tumor neoplasm of neck chronic bronchitis malignant ependymoma endometrial cancer benign neoplasm hypothyroidism prostate disease malignant tumor of neck endometriosis thrombotic disease bipolar disorder inborn carbohydrate metabolic disorder acute kidney failure maturity-onset diabetes of the young brain cancer interstitial lung disease congenital heart disease fallopian tube cancer invasive ductal breast carcinoma gastric cancer schizophrenia vertebral column disease limb-girdle muscular dystrophy depressive disorder arteriosclerosis disorder cataract diabetic kidney disease spondyloepiphyseal dysplasia tarda, X-linked myopathy cervical carcinoma major depressive disorder autoimmune disease hyperglycemia colonic neoplasm endophthalmitis blindness (disorder) Melnick-Needles syndrome brain hypoxia - ischemia intestinal disease brain injury retinal ischemia gastric carcinoma uterine disease obesity disorder cribriform carcinoma Schwartz-Jampel syndrome glaucoma breast disease ovarian cancer cystic fibrosis sinusitis pancreatic intraductal papillary-mucinous neoplasm

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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.

43NO | pdb_000043no

Crystal structure of a de novo-designed Binder targeting VEGFA

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation