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Human Metabolome Database Version 2.5

 

Showing metabocard for Hydrogen selenide (HMDB11110)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2008-10-16 23:28:01
Update Date 2009-05-05 21:06:59
Accession Number HMDB11110
Secondary Accession Numbers Not Available
Common Name Hydrogen selenide
Description Hydrogen selenide is a metabolite of selenium which could have potential antiangiogenic effect in the chemoprevention of cancer. The hydrogen selenide is a key intermediate in the selenium methylation metabolism of inorganic and organic selenium compounds. Accumulation of the hydrogen selenide resulting from inhibition of the selenium methylation metabolism, detoxification metabolic pathway of selenium, is found in animals following repeated administration of a toxic dose of selenocystine. The excess of the hydrogen selenide produced by inhibition of the selenium methylation metabolism contributes to the hepatotoxicity caused by selenocystine. (PMID: 9414580, 11799926)
Synonyms
  1. Dihydrogen monoselenide
  2. Dihydrogen selenide
  3. Hydrogen selenide
  4. Selane
  5. Selenium dihydride
  6. Selenium hydride
  7. Selenium hydride (SeH2)
Chemical IUPAC Name hydrogen selenide
Chemical Formula H2Se
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Inorganic
Super Class
—
Class
—
Sub Class
—
Family
  • Mammalian Metabolite
Species
—
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 80.976
Monoisotopic Molecular Weight 81.932175
Isomeric SMILES [SeH2]
Canonical SMILES [SeH2]
KEGG Compound ID C01528 Link Image
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB11110 Link Image
Metagene Link HMDB11110 Link Image
METLIN ID Not Available
PubChem Compound 533 Link Image
PubChem Substance 8144677 Link Image
ChEBI ID Not Available
CAS Registry Number Not Available
InChI Identifier InChI=1/H2Se/h1H2
Synthesis Reference Not Available
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility Not Available Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity Not Available Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Not Available
Not Available
Predicted 13C NMR Spectrum Not Available
Not Available
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location Not Available
Biofluid Location Not Available
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Selenoamino Acid Metabolism SMP00029 Link Image map00450 Link Image
General References Not Available
Metabolic Enzymes
  1. Selenide, water dikinase 1
  2. Selenide, water dikinase 2
  3. Selenocysteine lyase
Enzyme 1 [top]
Enzyme 1 ID 5925
Enzyme 1 Name Selenide, water dikinase 1
Enzyme 1 Synonyms
  1. Selenophosphate synthetase 1
  2. Selenium donor protein 1
Enzyme 1 Gene Name SEPHS1
Enzyme 1 Protein Sequence >Selenide, water dikinase 1 
MSTRESFNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAV
MPRLGIGMDTCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECD
NMLMLLGVSNKMTDRERDKVMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVC
QPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQWLDIPEKWNKIKLVVTQEDVELAYQEA
MMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRNEVSFVIHNLPVLAKMA
AVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQAWIIGIVEKG
NRTARIIDKPRIIEVAPQVATQNVNPTPGATS
Enzyme 1 Number of Residues 392
Enzyme 1 Molecular Weight 42911
Enzyme 1 Theoretical pI 5.84
Enzyme 1 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • kinase activity
  • nucleotide binding
  • purine nucleotide binding
  • selenide, water dikinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
—
Component
—
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function Synthesizes selenophosphate from selenide and ATP
Enzyme 1 Pathways
Enzyme 1 Reactions
  • ATP + selenide + H2O = AMP + selenophosphate + phosphate
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 1000284 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P49903 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name SPS1_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1152 bp 
ATGTCTACGCGGGAGTCCTTTAACCCGGAAAGTTACGAATTGGACAAAAGCTTCCGGCTA
ACCAGATTCACTGAACTGAAGGGCACAGGCTGCAAAGTGCCCCAAGATGTCCTGCAAAAA
TTGCTGGAATCTTTACAGGAGAACCACTTCCAAGAAGATGAGCAGTTTCTGGGAGCCGTT
ATGCCAAGGCTTGGCATTGGAATGGATACTTGTGTCATTCCTTTGAGGCACGGTGGGCTT
TCCTTGGTTCAAACCACAGATTACATTTACCCGATCGTAGACGACCCTTACATGATGGGC
AGGATAGCGTGTGCCAATGTCCTCAGTGACCTCTATGCAATGGGGGTCACGGAATGTGAC
AATATGCTGATGCTCCTTGGAGTCAGTAATAAAATGACCGACAGGGAAAGGGATAAAGTG
ATGCCTCTGATTATCCAAGGTTTTAAAGACGCAGCTGAGGAAGCAGGAACGTCTGTAACA
GGCGGCCAAACAGTACTAAACCCCTGGATTGTCCTGGGAGGAGTGGCTACCACTGTCTGC
CAACCCAATGAATTTATCATGCCAGACAATGCAGTGCCAGGGGACGTGCTGGTGCTGACA
AAACCCCTGGGGACACAGGTGGCAGTGGCTGTGCACCAGTGGCTGGATATCCCTGAGAAA
TGGAATAAGATTAAACTAGTGGTCACCCAAGAAGATGTAGAGCTGGCCTACCAGGAGGCG
ATGATGAACATGGCGAGGCTCAACAGGACAGCTGCAGGACTCATGCACACGTTCAATACC
CACGCCGCCACTGACATCACGGGCTTCGGGATTTTGGGCCATGCGCAGAACCTGGCCAAG
CAGCAGAGGAACGAGGTGTCGTTTGTAATTCACAACCTCCCGGTGCTGGCCAAGATGGCT
GCGGTGAGCAAGGCCTGCGGAAACATGTTCGGCCTCATGCACGGGACCTGCCCGGAGACT
TCAGGCGGCCTTCTGATCTGTTTACCACGTGAGCAAGCAGCTCGGTTCTGTGCAGAGATA
AAGTCCCCCAAATATGGTGAAGGCCACCAAGCATGGATTATTGGGATTGTAGAGAAGGGC
AACCGCACAGCCAGAATCATAGACAAACCCCGGATCATCGAGGTCGCACACAAGTGGCCA
CTCAAAACGTGA
Enzyme 1 GenBank Gene ID U34044 Link Image
Enzyme 1 GeneCard ID SEPHS1 Link Image
Enzyme 1 GenAtlas ID SEPHS1 Link Image
Enzyme 1 HGNC ID HGNC:19685 Link Image
Enzyme 1 Chromosome Location 10
Enzyme 1 Locus 10p14
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Low SC, Harney JW, Berry MJ: Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis. J Biol Chem. 1995 Sep 15;270(37):21659-64. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 5930
Enzyme 2 Name Selenide, water dikinase 2
Enzyme 2 Synonyms
  1. Selenophosphate synthetase 2
  2. Selenium donor protein 2
Enzyme 2 Gene Name SEPHS2
Enzyme 2 Protein Sequence >Selenide, water dikinase 2 
MAEASATGACGEAMAAAEGSSGPAGLTLGRSFSNYRPFEPQALGLSPSWRLTGFSGMKGC
GCKVPQEALLKLLAGLTRPDVRPPLGRGLVGGQEEASQEAGLPAGAGPSPTFPALGIGMD
SCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVS
QSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPD
SAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNR
TAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRF
GLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKP
RVIEVLPRGATAAVLAPDSSNASSEPSS
Enzyme 2 Number of Residues 448
Enzyme 2 Molecular Weight 47259
Enzyme 2 Theoretical pI 5.69
Enzyme 2 GO Classification
Function
  • ATP binding
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • kinase activity
  • nucleotide binding
  • purine nucleotide binding
  • selenide, water dikinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
—
Component
—
Enzyme 2 General Function Amino acid transport and metabolism
Enzyme 2 Specific Function Synthesizes selenophosphate from selenide and ATP
Enzyme 2 Pathways
Enzyme 2 Reactions
  • ATP + selenide + H2O = AMP + selenophosphate + phosphate
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 14717790 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q99611 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name SPS2_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >1347 bp 
ATGGCGGAAGCCTCGGCGACGGGCGCCTGCGGAGAGGCGATGGCAGCGGCGGAAGGCTCC
TCGGGCCCGGCGGGCTTGACTCTGGGCCGGAGCTTCTCGAACTACCGGCCCTTCGAGCCC
CAGGCGTTGGGCCTCAGCCCGAGCTGGCGGCTGACGGGCTTCTCCGGCATGAAGGGCTGA
GGCTGCAAGGTCCCGCAGGAGGCGCTGCTCAAACTCCTGGCGGGACTGACGCGGCCGGAC
GTGCGGCCCCCGCTGGGCCGGGGCCTGGTGGGTGGCCAGGAAGAGGCGTCCCAGGAAGCC
GGCCTGCCGGCAGGAGCGGGCCCCAGCCCCACCTTTCCAGCCCTGGGCATCGGGATGGAC
TCCTGCGTCATCCCCCTGAGGCACGGGGGCCTGTCACTGGTGCAGACCACGGACTTCTTT
TACCCCTTGGTAGAAGATCCCTACATGATGGGGCGCATAGCTTGTGCCAACGTGCTGAGT
GACCTCTACGCCATGGGGATTACTGAGTGTGACAACATGTTGATGTTACTCAGCGTCAGC
CAGAGTATGAGTGAGGAGGAACGCGAAAAGGTAACGCCACTCATGGTCAAAGGCTTTCGG
GATGCGGCTGAGGAAGGAGGGACGGCAGTGACCGGTGGGCAAACGGTGGTCAACCCTTGG
ATTATAATCGGTGGAGTTGCCACTGTAGTATGCCAACCAAATGAGTTCATAATGCCGGAC
AGCGCCGTCGTTGGGGACGTGCTGGTGTTAACCAAACCGTTAGGAACCCAGGTTGCTGTC
AATGCCCACCAATGGCTGGATAATCCTGAAAGATGGAATAAAGTAAAGATGGTGGTCTCC
AGAGAAGAGGTGGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGCTACCCTCAACAGA
ACTGCTGCAGGTTTAATGCACACATTTAATGCCCATGCGGCCACAGATATCACAGGCTTT
GGCATTCTAGGACACTCCCAGAACCTTGCAAAACAACAAAGAAATGAAGTGTCCTTTGTT
ATTCATAATCTGCCAATAATTGCCAAGATGGCTGCCGTCAGCAAGGCCAGTGGACGGTTT
GGGCTTCTTCAAGGAACCTCAGCTGAAACCTCTGGGGGATTACTGATTTGTCTGCCAAGA
GAACAGGCGGCTCGCTTTTGTTCTGAAATCAAATCCTCCAAGTACGGAGAGGGTCACCAA
GCGTGGATCGTTGGCATTGTGGAAAAGGGAAACCGAACGGCCCGGATCATTGACAAGCCG
CGAGTTATTGAAGTCCTGCCTCGTGGGGCCACAGCTGCTGTTCTTGCTCCTGACAGTTCA
AATGCCTCCTCTGAGCCTAGCTCGTGA
Enzyme 2 GenBank Gene ID U43286 Link Image
Enzyme 2 GeneCard ID SEPHS2 Link Image
Enzyme 2 GenAtlas ID SEPHS2 Link Image
Enzyme 2 HGNC ID HGNC:19686 Link Image
Enzyme 2 Chromosome Location 16
Enzyme 2 Locus 16p11.2
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Guimaraes MJ, Bazan JF, Zlotnik A, Wiles MV, Grimaldi JC, Lee F, McClanahan T: A new approach to the study of haematopoietic development in the yolk sac and embryoid bodies. Development. 1995 Oct;121(10):3335-46. [PubMed Link Image]
  2. Guimaraes MJ, Peterson D, Vicari A, Cocks BG, Copeland NG, Gilbert DJ, Jenkins NA, Ferrick DA, Kastelein RA, Bazan JF, Zlotnik A: Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism? Proc Natl Acad Sci U S A. 1996 Dec 24;93(26):15086-91. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 10418
Enzyme 3 Name Selenocysteine lyase
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name SCLY
Enzyme 3 Protein Sequence >Selenocysteine lyase 
MEAAVAPGRDAPAPAASQPSGCGKHNSPERKVYMDYNATTPLEPEVIQAMTKAMWEAWGN
PSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHANQTS
KGHTGGHHSPVKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTEVDDI
LAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALNQERVAAGLPPILVHTDAAQALGK
QRVDVEDLGVDFLTIVGHKFYGPRIGALYIRGLGEFTPLYPMLFGGGQERNFRPGTENTP
MIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFGQKRIHLNSQFPGTQRLPNTCN
FSIRGPRLQGHVVLAQCRVLMASVGAACHSDHGDQPSPVLLSYGVPFDVARNALRLSVGR
STTRAEVDLVVQDLKQAVAQLEDQA
Enzyme 3 Number of Residues 445
Enzyme 3 Molecular Weight 48179
Enzyme 3 Theoretical pI Not Available
Enzyme 3 GO Classification
Function
  • catalytic activity
  • transaminase activity
  • transferase activity
  • transferase activity, transferring nitrogenous groups
Process
  • metabolism
  • physiological process
Component
—
Enzyme 3 General Function Amino acid transport and metabolism
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions
  • Pyridoxine 5'-phosphate + Selenocysteine --> L-Alanine + H+ + Pyridoxal 5'-phosphate + Selenide
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein 14043901 Link Image
Enzyme 3 UniProtKB/Swiss-Prot ID Q96I15 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name Q96I15_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID BC007891 Link Image
Enzyme 3 GeneCard ID Not Available
Enzyme 3 GenAtlas ID SCLY Link Image
Enzyme 3 HGNC ID HGNC:18161 Link Image
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References
  1. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA: Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11. [PubMed Link Image]
Enzyme 3 Metabolite References Not Available