3VZD | pdb_00003vzd

Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	KOG1116	e3vzdF5	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
F	DAGK_cat	e3vzdF6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
E	KOG1116	e3vzdE5	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
E	DAGK_cat	e3vzdE6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
D	KOG1116	e3vzdD5	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
D	DAGK_cat	e3vzdD6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
C	KOG1116	e3vzdC5	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
C	DAGK_cat	e3vzdC6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
B	KOG1116	e3vzdB5	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
B	DAGK_cat	e3vzdB6	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)
A	KOG1116	e3vzdA1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: KOG1116	ECOD (1.6)
A	DAGK_cat	e3vzdA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: DAGK_cat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
F	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
E	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
E	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
D	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
D	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
C	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
C	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
B	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
B	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
A	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
A	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00781	Diacylglycerol kinase catalytic domain (DAGK_cat)	Diacylglycerol kinase catalytic domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Sphingosine kinase 1	bioactive lipid receptor activity sphingosine-1-phosphate receptor activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity kinase activity lipid kinase activity transferase activity, transferring phosphorus-containing groups bioactive lipid receptor activity sphingosine-1-phosphate receptor activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity kinase activity lipid kinase activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding protein binding calmodulin binding protein phosphatase binding phosphatase binding enzyme binding protein phosphatase 2A binding sphingosine kinase activity phosphotransferase activity, alcohol group as acceptor cation binding magnesium ion binding metal ion binding lipid binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of localization import into cell regulation of biological process regulation of cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of localization import into cell regulation of biological process regulation of cellular process regulation of cellular component organization regulation of transport transport biological regulation regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization localization cellular process cellular component organization or biogenesis endocytosis regulation of endocytosis cell population proliferation membrane lipid metabolic process polyol metabolic process sphingolipid metabolic process primary metabolic process alcohol metabolic process sphingosine metabolic process sphingoid metabolic process diol metabolic process metabolic process small molecule metabolic process lipid metabolic process regulation of defense response response to stimulus regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus regulation of response to stimulus response to stress regulation of response to stress regulation of neuroinflammatory response inflammatory response neuroinflammatory response positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle regulation of mitotic cell cycle positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process macromolecule metabolic process DNA biosynthetic process regulation of phagocytosis phagocytosis positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process RNA biosynthetic process positive regulation of molecular function DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression regulation of molecular function regulation of gene expression regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process vasculature development blood vessel development circulatory system development regulation of interleukin-1 production interleukin-1 production regulation of interleukin-1 beta production interleukin-1 beta production regulation of cytokine production cytokine production regulation of multicellular organismal process cellular response to stimulus signaling response to cytokine regulation of signal transduction cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction regulation of signaling regulation of tumor necrosis factor-mediated signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway response to peptide regulation of response to cytokine stimulus response to chemical regulation of cell communication response to tumor necrosis factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor regulation of growth growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process diol biosynthetic process sphingosine biosynthetic process polyol biosynthetic process alcohol biosynthetic process membrane lipid biosynthetic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-threonine phosphorylation positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process peptidyl-threonine modification positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of peptidyl-threonine phosphorylation phosphorylation regulation of protein metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation peptidyl-threonine phosphorylation regulation of macrophage activation regulation of leukocyte activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response regulation of immune system process cell activation immune system process microglial cell activation regulation of microglial cell activation glial cell activation fibroblast proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation sphingolipid catabolic process lipid catabolic process catabolic process sphingoid catabolic process membrane lipid catabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of amide metabolic process regulation of lipid metabolic process negative regulation of lipid biosynthetic process cellular component biogenesis regulation of sphingolipid biosynthetic process amide metabolic process regulation of ceramide biosynthetic process negative regulation of sphingolipid biosynthetic process ceramide metabolic process regulation of membrane lipid metabolic process negative regulation of amide metabolic process negative regulation of metabolic process amide biosynthetic process regulation of cellular component biogenesis negative regulation of ceramide biosynthetic process negative regulation of biosynthetic process ceramide biosynthetic process regulation of lipid biosynthetic process negative regulation of lipid metabolic process intracellular signal transduction calcium-mediated signaling intracellular signaling cassette cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress protein acetylation protein acylation regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling system process positive regulation of smooth muscle contraction regulation of system process muscle contraction muscle system process regulation of muscle system process smooth muscle contraction regulation of muscle contraction regulation of smooth muscle contraction positive regulation of muscle contraction positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process interleukin-17 production regulation of interleukin-17 production positive regulation of gene expression positive regulation of interleukin-17 production positive regulation of cytokine production p38MAPK cascade positive regulation of MAPK cascade regulation of MAPK cascade positive regulation of p38MAPK cascade regulation of p38MAPK cascade MAPK cascade endosomal vesicle fusion membrane fusion organelle membrane fusion regulation of vesicle fusion regulation of endosomal vesicle fusion vesicle organization membrane organization organelle fusion vesicle fusion positive regulation of mitotic cell cycle	cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle endocytic vesicle cell projection cilium plasma membrane bounded cell projection cell periphery plasma membrane presynapse synapse cell junction nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome membrane early endosome endosome early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR016064	NAD kinase/diacylglycerol kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001206	Diacylglycerol kinase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050187	Lipid Phosphate Formation and Regulation	Family
A, B, C, D, E A, B, C, D, E, F	IPR017438	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q9NYA1	myelodysplastic syndrome ulcerative colitis Fibrosis leukemia glioblastoma malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis malignant glioma osteosarcoma psoriasis medulloblastoma ovarian cancer tuberculosis

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.