4Q6R

Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile

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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KOG1383	e4q6rA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: KOG1383	ECOD (1.6)
A	Aminotran_5_N	e4q6rA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	KOG1383	e4q6rB2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: KOG1383	ECOD (1.6)
B	Aminotran_5_N	e4q6rB1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.140.2150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	6.10.140.2150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00282	Pyridoxal-dependent decarboxylase conserved domain (Pyridoxal_deC)	Pyridoxal-dependent decarboxylase conserved domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Sphingosine-1-phosphate lyase 1	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding sphinganine-1-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity	developmental process multicellular organismal process gonad development reproductive system development cellular developmental process reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics cell differentiation developmental process multicellular organismal process gonad development reproductive system development cellular developmental process reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics cell differentiation anatomical structure development reproductive structure development cellular process Leydig cell differentiation system development spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation regulation of hormone levels steroid metabolic process biological regulation androgen metabolic process primary metabolic process hormone metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process regulation of biological quality lipid metabolic process anatomical structure morphogenesis head development face morphogenesis head morphogenesis face development body morphogenesis estrogen metabolic process hemopoiesis cell development ameboidal-type cell migration cell migration fibroblast migration cell motility regulation of multicellular organism growth regulation of biological process regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth multicellular organism growth regulation of multicellular organismal process cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway fatty acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process cellular lipid metabolic process small molecule metabolic process monocarboxylic acid metabolic process membrane lipid metabolic process organonitrogen compound metabolic process sphingolipid metabolic process blood vessel morphogenesis tube development vasculogenesis vasculature development circulatory system development tube morphogenesis blood vessel development skeletal system development skeletal system morphogenesis animal organ morphogenesis sphingolipid catabolic process organonitrogen compound catabolic process catabolic process lipid catabolic process membrane lipid catabolic process cellular lipid catabolic process cellular catabolic process organic substance catabolic process cell death apoptotic signaling pathway apoptotic process programmed cell death ceramide metabolic process amide metabolic process kidney development renal system development post-embryonic development roof of mouth development rhythmic process ovulation cycle process luteinization female gonad development female sex differentiation development of primary female sexual characteristics ovulation cycle	membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane cellular anatomical entity intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002129	Pyridoxal phosphate-dependent decarboxylase	Family
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O95470	nephrotic syndrome 14 adrenoleukodystrophy Disorders of Sex Development intellectual disability lung cancer medulloblastoma ovarian cancer pituitary cancer astrocytic tumor glioblastoma interstitial cystitis lung carcinoma pancreatic intraductal papillary-mucinous carcinoma X-linked adrenal hypoplasia congenita Charcot-Marie-Tooth disease nephrotic syndrome 14 adrenoleukodystrophy Disorders of Sex Development intellectual disability lung cancer medulloblastoma ovarian cancer pituitary cancer astrocytic tumor glioblastoma interstitial cystitis lung carcinoma pancreatic intraductal papillary-mucinous carcinoma X-linked adrenal hypoplasia congenita Charcot-Marie-Tooth disease hydrops fetalis invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma pilocytic astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.