MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
1KEX	1.9	Crystal Structure of the b1 Domain of Human Neuropilin-1
2QQI	1.8	Crystal Structure of the b1b2 Domains from Human Neuropilin-1
2QQM	2.0	Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1
2QQN	2.2	Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab
3I97	2.9	B1 domain of human Neuropilin-1 bound with small molecule EG00229
4DEQ	2.649	Structure of the Neuropilin-1/VEGF-A complex
4RN5	1.73	B1 domain of human Neuropilin-1 with acetate ion in a ligand-binding site
5C7G	1.45	Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule
5IJR	1.52	X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
5IYY	1.6	X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
5J1X	2.1	X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand.
5JGI	1.38	X-ray structure of neuropilin-1 b1 domain complexed with M45 compound
5JGQ	1.6	X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.
5JHK	1.8	X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand.
5L73	2.24	MAM domain of human neuropilin-1
6FMC	0.9	Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure
6FMF	2.811	Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure
6TKK	1.06	Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
7JJC	2.36	Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide
7O1N	1.56	Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
7P5U	1.6	Neuropilin-b1 in a complex with a VEGFB-derived peptide

GO term

GO ontology	GO term	GO description
Biological Process	GO:0038190	VEGF-activated neuropilin signaling pathway
Biological Process	GO:1902378	VEGF-activated neuropilin signaling pathway involved in axon guidance
Biological Process	GO:0001525	angiogenesis
Biological Process	GO:0060978	angiogenesis involved in coronary vascular morphogenesis
Biological Process	GO:0009887	animal organ morphogenesis
Biological Process	GO:0048844	artery morphogenesis
Biological Process	GO:0048846	axon extension involved in axon guidance
Biological Process	GO:0007411	axon guidance
Biological Process	GO:0007413	axonal fasciculation
Biological Process	GO:0060385	axonogenesis involved in innervation
Biological Process	GO:0150020	basal dendrite arborization
Biological Process	GO:0150018	basal dendrite development
Biological Process	GO:0001569	branching involved in blood vessel morphogenesis
Biological Process	GO:0021785	branchiomotor neuron axon guidance
Biological Process	GO:0002042	cell migration involved in sprouting angiogenesis
Biological Process	GO:0007267	cell-cell signaling
Biological Process	GO:0035729	cellular response to hepatocyte growth factor stimulus
Biological Process	GO:0035924	cellular response to vascular endothelial growth factor stimulus
Biological Process	GO:0071679	commissural neuron axon guidance
Biological Process	GO:0060982	coronary artery morphogenesis
Biological Process	GO:0060666	dichotomous subdivision of terminal units involved in salivary gland branching
Biological Process	GO:1904835	dorsal root ganglion morphogenesis
Biological Process	GO:0035767	endothelial cell chemotaxis
Biological Process	GO:0043542	endothelial cell migration
Biological Process	GO:0097102	endothelial tip cell fate specification
Biological Process	GO:0021612	facial nerve structural organization
Biological Process	GO:1903375	facioacoustic ganglion development
Biological Process	GO:0021828	gonadotrophin-releasing hormone neuronal migration to the hypothalamus
Biological Process	GO:0048012	hepatocyte growth factor receptor signaling pathway
Biological Process	GO:0007229	integrin-mediated signaling pathway
Biological Process	GO:0097475	motor neuron migration
Biological Process	GO:0048843	negative regulation of axon extension involved in axon guidance
Biological Process	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway
Biological Process	GO:0043524	negative regulation of neuron apoptotic process
Biological Process	GO:0021675	nerve development
Biological Process	GO:0001755	neural crest cell migration
Biological Process	GO:1901166	neural crest cell migration involved in autonomic nervous system development
Biological Process	GO:0001764	neuron migration
Biological Process	GO:0038189	neuropilin signaling pathway
Biological Process	GO:1905040	otic placode development
Biological Process	GO:0003148	outflow tract septum morphogenesis
Biological Process	GO:0048008	platelet-derived growth factor receptor signaling pathway
Biological Process	GO:0050918	positive chemotaxis
Biological Process	GO:0070374	positive regulation of ERK1 and ERK2 cascade
Biological Process	GO:0045766	positive regulation of angiogenesis
Biological Process	GO:0048842	positive regulation of axon extension involved in axon guidance
Biological Process	GO:0090050	positive regulation of cell migration involved in sprouting angiogenesis
Biological Process	GO:0060301	positive regulation of cytokine activity
Biological Process	GO:0010595	positive regulation of endothelial cell migration
Biological Process	GO:0001938	positive regulation of endothelial cell proliferation
Biological Process	GO:0051491	positive regulation of filopodium assembly
Biological Process	GO:0051894	positive regulation of focal adhesion assembly
Biological Process	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation
Biological Process	GO:0042327	positive regulation of phosphorylation
Biological Process	GO:1902336	positive regulation of retinal ganglion cell axon guidance
Biological Process	GO:0014911	positive regulation of smooth muscle cell migration
Biological Process	GO:0051496	positive regulation of stress fiber assembly
Biological Process	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading
Biological Process	GO:0099173	postsynapse organization
Biological Process	GO:1902946	protein localization to early endosome
Biological Process	GO:0032489	regulation of Cdc42 protein signal transduction
Biological Process	GO:0090259	regulation of retinal ganglion cell axon guidance
Biological Process	GO:0030947	regulation of vascular endothelial growth factor receptor signaling pathway
Biological Process	GO:0060627	regulation of vesicle-mediated transport
Biological Process	GO:0061441	renal artery morphogenesis
Biological Process	GO:0009611	response to wounding
Biological Process	GO:0061299	retina vasculature morphogenesis in camera-type eye
Biological Process	GO:0031290	retinal ganglion cell axon guidance
Biological Process	GO:0071526	semaphorin-plexin signaling pathway
Biological Process	GO:1902287	semaphorin-plexin signaling pathway involved in axon guidance
Biological Process	GO:1902285	semaphorin-plexin signaling pathway involved in neuron projection guidance
Biological Process	GO:0097374	sensory neuron axon guidance
Biological Process	GO:0007165	signal transduction
Biological Process	GO:0002040	sprouting angiogenesis
Biological Process	GO:0034446	substrate adhesion-dependent cell spreading
Biological Process	GO:0006930	substrate-dependent cell migration, cell extension
Biological Process	GO:0061549	sympathetic ganglion development
Biological Process	GO:0097490	sympathetic neuron projection extension
Biological Process	GO:0097491	sympathetic neuron projection guidance
Biological Process	GO:1901998	toxin transport
Biological Process	GO:0061551	trigeminal ganglion development
Biological Process	GO:0021637	trigeminal nerve structural organization
Biological Process	GO:0048010	vascular endothelial growth factor receptor signaling pathway
Biological Process	GO:0001570	vasculogenesis
Biological Process	GO:0036486	ventral trunk neural crest cell migration
Biological Process	GO:0021649	vestibulocochlear nerve structural organization
Biological Process	GO:0046718	viral entry into host cell
Molecular Function	GO:0005096	GTPase activator activity
Molecular Function	GO:0015026	coreceptor activity
Molecular Function	GO:0019955	cytokine binding
Molecular Function	GO:0019838	growth factor binding
Molecular Function	GO:0008201	heparin binding
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:0019901	protein kinase binding
Molecular Function	GO:0017154	semaphorin receptor activity
Molecular Function	GO:0038085	vascular endothelial growth factor binding
Molecular Function	GO:0005021	vascular endothelial growth factor receptor activity
Cellular Component	GO:0030424	axon
Cellular Component	GO:0031410	cytoplasmic vesicle
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0005769	early endosome
Cellular Component	GO:0005615	extracellular space
Cellular Component	GO:0005925	focal adhesion
Cellular Component	GO:0098978	glutamatergic synapse
Cellular Component	GO:0031966	mitochondrial membrane
Cellular Component	GO:0005883	neurofilament
Cellular Component	GO:0043005	neuron projection
Cellular Component	GO:0005886	plasma membrane
Cellular Component	GO:0045211	postsynaptic membrane
Cellular Component	GO:0043235	receptor complex
Cellular Component	GO:0002116	semaphorin receptor complex
Cellular Component	GO:0097443	sorting endosome

InterPro / Pfam

InterPro	InterPro name
IPR000421	Coagulation factor 5/8 C-terminal domain
IPR000859	CUB domain
IPR000998	MAM domain
IPR008979	Galactose-binding-like domain superfamily
IPR013320	Concanavalin A-like lectin/glucanase domain superfamily
IPR014648	Neuropilin
IPR022579	Neuropilin, C-terminal
IPR035914	Spermadhesin, CUB domain superfamily

Pfam	Pfam name
PF00431	CUB domain
PF00629	MAM domain, meprin/A5/mu
PF00754	F5/8 type C domain
PF11980	C-terminal domain of neuropilin glycoprotein

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-194306	Neurophilin interactions with VEGF and VEGFR	Leaf	R-HSA-162582	Signal Transduction
R-HSA-376176	Signaling by ROBO receptors	Internal node	R-HSA-1266738	Developmental Biology
R-HSA-399954	Sema3A PAK dependent Axon repulsion	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-399955	SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-399956	CRMPs in Sema3A signaling	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-445144	Signal transduction by L1	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-447041	CHL1 interactions	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-9694614	Attachment and Entry	Leaf	R-HSA-1643685	Disease

Subcellular location

Location	ECO term	Pubmed
Cell membrane	ECO:0000269	PubMed:30623799
Cytoplasm	ECO:0000269	PubMed:30623799
Mitochondrion membrane	ECO:0000305	PubMed:30623799
Secreted	ECO:0000269	PubMed:10688880

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	Medium	Approved
appendix	glandular cells	Medium	Approved
appendix	lymphoid tissue	Low	Approved
bone marrow	hematopoietic cells	Medium	Approved
breast	glandular cells	Medium	Approved
breast	myoepithelial cells	Medium	Approved
bronchus	ciliated cells (cell body)	Low	Approved
bronchus	ciliated cells (ciliary rootlets)	High	Approved
bronchus	ciliated cells (tip of cilia)	High	Approved
caudate	glial cells	Low	Approved
caudate	neuronal cells	Low	Approved
cerebellum	Purkinje cells	Low	Approved
cerebellum	cells in granular layer	Low	Approved
cerebellum	cells in molecular layer	Low	Approved
cerebral cortex	glial cells	Low	Approved
cerebral cortex	neuronal cells	Low	Approved
cerebral cortex	neuropil	Low	Approved
cervix	glandular cells	Low	Approved
colon	endothelial cells	Low	Approved
colon	glandular cells	Medium	Approved
colon	peripheral nerve/ganglion	Medium	Approved
duodenum	glandular cells	Medium	Approved
endometrium 1	glandular cells	Medium	Approved
endometrium 2	glandular cells	Low	Approved
esophagus	squamous epithelial cells	Medium	Approved
fallopian tube	ciliated cells (cell body)	Low	Approved
fallopian tube	ciliated cells (tip of cilia)	High	Approved
gallbladder	glandular cells	Medium	Approved
heart muscle	cardiomyocytes	Low	Approved
hippocampus	neuronal cells	Low	Approved
kidney	cells in tubules	Medium	Approved
liver	hepatocytes	Medium	Approved
lung	macrophages	Low	Approved
lymph node	germinal center cells	Medium	Approved
lymph node	non-germinal center cells	Medium	Approved
nasopharynx	ciliated cells (cell body)	Low	Approved
nasopharynx	ciliated cells (tip of cilia)	High	Approved
pancreas	exocrine glandular cells	Medium	Approved
parathyroid gland	glandular cells	Medium	Approved
placenta	trophoblastic cells	Medium	Approved
rectum	glandular cells	Medium	Approved
salivary gland	glandular cells	Low	Approved
seminal vesicle	glandular cells	Low	Approved
skin 1	melanocytes	Low	Approved
skin 2	epidermal cells	Low	Approved
small intestine	glandular cells	Medium	Approved
smooth muscle	smooth muscle cells	Medium	Approved
soft tissue 2	peripheral nerve	Low	Approved
spleen	cells in red pulp	Medium	Approved
spleen	cells in white pulp	Low	Approved
stomach 1	glandular cells	Medium	Approved
stomach 2	glandular cells	Medium	Approved
testis	Leydig cells	Medium	Approved
testis	cells in seminiferous ducts	Low	Approved
thyroid gland	glandular cells	Low	Approved
tonsil	germinal center cells	Low	Approved
tonsil	non-germinal center cells	Low	Approved
vagina	squamous epithelial cells	Low	Approved

Summary of O14786

Gene: NRP1, NRP, VEGF165R
Protein: Neuropilin-1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of O14786

Gene: NRP1, NRP, VEGF165R Protein: Neuropilin-1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: NRP1, NRP, VEGF165R
Protein: Neuropilin-1