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Human Metabolome Database Version 2.5

 

Showing metabocard for GDP-4-Dehydro-6-deoxy-D-mannose (HMDB01346)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:58:45
Accession Number HMDB01346
Secondary Accession Numbers HMDB01391
Common Name GDP-4-Dehydro-6-deoxy-D-mannose
Description GDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in the fucosylation of mammalian cells. The functional significance of these fucosylated glycans is unclear, although there is evidence that the sialyl Lex determinant participaates in leukocyte adhesion and trafficking processes. GDP-4-Dehydro-6-deoxy-D-mannose is generated by GDP-D-mannose-4,6-dehydratase (GMD). This compound is then converted by the FX protein (GDP-4-keto-6-D-deoxymannose epimerase/GDP-4-keto-6-L-galactose reductase) to GDP-L-fucose. (PMID: 11698403)
Synonyms
  1. GDP-4-dehydro-6-deoxy-D-mannose
  2. GDP-4-dehydro-6-deoxy-D-talose
  3. GDP-4-dehydro-D-rhamnose
  4. GDP-4-keto-6-deoxy-D-mannose
  5. GDP-4-keto-6-deoxymannose
  6. GDP-4-oxo-6-deoxy-D-mannose
  7. GDP-4-oxo-6-deoxymannose
  8. Guanosine diphosphate-4-keto-6-deoxy-D-mannose
  9. GDP-4-keto-6-D-deoxymannose
Chemical IUPAC Name [(2S,3S,4R,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[(2R,3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxo-oxan-2-yl]oxy-hydroxy-phosphoryl]oxy-phosphinic acid
Chemical Formula C16H23N5O15P2
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Nucleosides and Nucleoside conjugates
Class
  • Nucleotides
Sub Class
  • Nucleotide diphosphates
Family
  • Mammalian Metabolite
Species
  • ketone
  • secondary alcohol
  • 1,2-diol
  • primary amine
  • primary aromatic amine
  • oxo(het)arene
  • phosphoric acid ester
  • aromatic compound
  • heterocyclic compound
Biofunction
  • Component of Fructose and mannose metabolism
Application
—
Source
  • Endogenous
Average Molecular Weight 587.326
Monoisotopic Molecular Weight 587.066589
Isomeric SMILES C[C@H]1O[C@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@@H](O)C1=O
Canonical SMILES CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2N=C(N)NC3=O)C(O)C(O)C1=O
KEGG Compound ID C01222 Link Image
BioCyc ID GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE Link Image
BiGG ID 37116 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB01346 Link Image
Metagene Link HMDB01346 Link Image
METLIN ID 6180 Link Image
PubChem Compound 439446 Link Image
PubChem Substance 4444 Link Image
ChEBI ID 16955 Link Image
CAS Registry Number 18186-48-6
InChI Identifier InChI=1/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1
Synthesis Reference Oths, Philip J.; Mayer, Robert M.; Floss, Heinz G. Stereochemistry and mechanism of the GDP-mannose dehydratase reaction. Carbohydrate Research (1990), 198(1), 91-100.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 7.05 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -1.57 [Predicted by ALOGPS]; -5.1 [Predicted by PubChem via XLOGP] 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 Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
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
Fructose and Mannose Degradation SMP00064 Link Image map00051 Link Image
General References Not Available
Metabolic Enzymes
  1. GDP-mannose 4,6 dehydratase
  2. GDP-L-fucose synthetase
  3. cDNA, FLJ94122, Homo sapiens tissue specific transplantation antigen P35B (TSTA3),mRNA (Tissue specific transplantation antigen P35B, isoform CRA_b)
Enzyme 1 [top]
Enzyme 1 ID 5622
Enzyme 1 Name GDP-mannose 4,6 dehydratase
Enzyme 1 Synonyms
  1. GDP-D-mannose dehydratase
  2. GMD
Enzyme 1 Gene Name GMDS
Enzyme 1 Protein Sequence >GDP-mannose 4,6 dehydratase 
MAHAPARCPSARGSGDGEMGKPRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSF
NTGRIEHLYKNPQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDL
AEYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYG
AAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIYLGQLECFSL
GNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSVREFVEKSFLHIGKTIVWEG
KNENEVGRCKETGKVHVTVDLKYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVH
ADVELMRTNPNA
Enzyme 1 Number of Residues 372
Enzyme 1 Molecular Weight 41950
Enzyme 1 Theoretical pI 7.35
Enzyme 1 GO Classification
Function
  • GDP-mannose 4,6-dehydratase activity
  • NAD binding
  • binding
  • carbon-oxygen lyase activity
  • catalytic activity
  • coenzyme binding
  • cofactor binding
  • hydro-lyase activity
  • lyase activity
Process
  • biosynthesis
  • cellular metabolism
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleotide-sugar metabolism
  • physiological process
Component
—
Enzyme 1 General Function Cell wall/membrane/envelope biogenesis
Enzyme 1 Specific Function Conversion of GDP-D-mannose to GDP-4-keto-6-D- deoxymannose
Enzyme 1 Pathways
Enzyme 1 Reactions
  • GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 3005057 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID O60547 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name GMDS_HUMAN Link Image
Enzyme 1 PDB ID 1T2A Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1119 bp 
ATGGCACACGCACCGGCACGCTGCCCCAGCGCCCGGGGCTCCGGGGACGGCGAGATGGGC
AAGCCCAGGAACGTGGCGCTCATCACCGGTATCACAGGCCAGGATGGTTCCTACCTGGCT
GAGTTCCTGCTGGAGAAAGGCTATGAGGTCCATGGAATTGTACGGCGGTCCAGTTCATTT
AATACGGGTCGAATTGAGCATCTGTATAAGAATCCCCAGGCTCACATTGAAGGAAACATG
AAGTTGCACTATGGCGATCTCACTGACAGTACCTGCCTTGTGAAGATCATTAATGAAGTA
AAGCCCACAGAGATCTACAACCTTGGAGCCCAGAGCCACGTCAAAATTTCCTTTGACCTC
GCTGAGTACACTGCGGACGTTGACGGAGTTGGCACTCTACGACTTCTAGATGCAGTTAAG
ACTTGTGGCCTTATCAACTCTGTGAAGTTCTACCAAGCCTCAACAAGTGAACTTTATGGG
AAAGTGCAGGAAATACCCCAGAAGGAGACCACCCCTTTCTATCCCCGGTCACCCTATGGG
GCAGCAAAACTCTATGCCTATTGGATTGTGGTGAACTTCCGTGAGGCGTATAATCTCTTT
GCAGTGAACGGCATTCTCTTCAATCATGAGAGTCCCAGAAGAGGAGCTAATTTCGTTACT
CGAAAAATTAGCCGGTCAGTAGCTAAGATTTACCTTGGACAACTGGAATGTTTCAGTTTG
GGAAATCTGGATGCCAAACGAGATTGGGGCCATGCCAAGGACTATGTGGAGGCTATGTGG
TTGATGTTGCAGAATGATGAGCCGGAGGACTTCGTTATAGCTACTGGGGAGGTCCATAGT
GTCCGGGAATTTGTCGAGAAATCATTCTTGCACATTGGAAAAACCATTGTGTGGGAAGGA
AAGAATGAAAATGAAGTGGGCAGATGTAAAGAGACCGGCAAAGTTCACGTGACTGTGGAT
CTCAAGTACTACCGGCCAACTGAAGTGGACTTTCTGCAGGGCGACTGCACCAAAGCGAAA
CAGAAGCTGAACTGGAAGCCCCGGGTCGCTTTCGATGAGCTGGTGAGGGAGATGGTGCAC
GCCGACGTGGAGCTCATGAGGACAAACCCCAATGCCTGA
Enzyme 1 GenBank Gene ID AF042377 Link Image
Enzyme 1 GeneCard ID GMDS Link Image
Enzyme 1 GenAtlas ID GMDS Link Image
Enzyme 1 HGNC ID HGNC:4369 Link Image
Enzyme 1 Chromosome Location 6
Enzyme 1 Locus 6p25
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Sullivan FX, Kumar R, Kriz R, Stahl M, Xu GY, Rouse J, Chang XJ, Boodhoo A, Potvin B, Cumming DA: Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J Biol Chem. 1998 Apr 3;273(14):8193-202. [PubMed Link Image]
  2. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S: The DNA sequence and analysis of human chromosome 6. Nature. 2003 Oct 23;425(6960):805-11. [PubMed Link Image]
  3. Ohyama C, Smith PL, Angata K, Fukuda MN, Lowe JB, Fukuda M: Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells. J Biol Chem. 1998 Jun 5;273(23):14582-7. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 6213
Enzyme 2 Name GDP-L-fucose synthetase
Enzyme 2 Synonyms
  1. Protein FX
  2. Red cell NADP(H- binding protein
  3. GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4- reductase
Enzyme 2 Gene Name TSTA3
Enzyme 2 Protein Sequence >GDP-L-fucose synthetase 
MGEPQGSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDTAQTRALFEK
VQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPD
KTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNF
NIEDGHVLPGLIHKVHLAKSSGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPI
ILSVGEEDEVSIKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTP
FKQAVKETCAWFTDNYEQARK
Enzyme 2 Number of Residues 321
Enzyme 2 Molecular Weight 35893
Enzyme 2 Theoretical pI 6.59
Enzyme 2 GO Classification
Function
  • NAD binding
  • binding
  • catalytic activity
  • coenzyme binding
  • cofactor binding
Process
  • cellular metabolism
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleotide-sugar metabolism
  • physiological process
Component
—
Enzyme 2 General Function Cell wall/membrane/envelope biogenesis
Enzyme 2 Specific Function Two step NADP-dependent conversion of GDP-4-dehydro-6- deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction
Enzyme 2 Pathways
Enzyme 2 Reactions
  • GDP-L-fucose + NADP+ = GDP-4-dehydro-6-deoxy-D-mannose + NADPH + H+
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 1381179 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q13630 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name FCL_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >966 bp 
ATGGGTGAACCCCAGGGATCCATGCGGATTCTAGTGACAGGGGGCTCTGGGCTGGTAGGC
AAAGCCATCCAGAAGGTGGTAGCAGATGGAGCTGGACTTCCTGGAGAGGACTGGGTGTTT
GTCTCCTCTAAAGACGCCGATCTCACGGATACAGCACAGACCCGCGCCCTGTTTGAGAAG
GTCCAACCCACACACGTCATCCATCTTGCTGCAATGGTGGGGGGCCTGTTCCGGAATATC
AAATACAATTTGGACTTCTGGAGGAAAAACGTGCACATGAACGACAACGTCCTGCACTCG
GCCTTTGAGGTGGGGGCCCGCAAGGTGGTGTCCTGCCTGTCCACCTGTATCTTCCCTGAC
AAGACGACCTACCCGATAGATGAGACCATGATCCACAATGGGCCTCCCCACAACAGCAAT
TTTGGGTACTCGTATGCCAAGAGGATGATCGACGTGCAGAACAGGGCCTACTTCCAGCAG
TACGGCTGCACCTTCACCGCTGTCATCCCCACCAACGTTTTCGGGCCCCACGACAACTTC
AACATCGAGGATGGCCACGTGCTGCCTGGCCTCATCCACAAGGTGCACCTGGCCAAGAGC
AGCGGCTCGGCCCTGACGGTGTGGGGTACAGGGAATCCGCGGAGGCAGTTCATATACTCG
CTGGACCTGGCCCAGCTCTTTATCTGGGTCCTGCGGGAGTACAATGAAGTGGAGCCCATC
ATCCTCTCCGTGGGCGAGGAAGATGAGGTCTCCATCAAGGAGGCAGCCGAGGCGGTGGTG
GAGGCCATGGACTTCCATGGGGAAGTCACCTTTGATACAACCAAGTCGGATGGGCAGTTT
AAGAAGACAGCCAGTAACAGCAAGCTGAGGACCTACCTGCCCGACTTCCGGTTCACACCC
TTCAAGCAGGCGGTGAAGGAGACCTGTGCTTGGTTCACTGACAACTACGAGCAGGCCCGG
AAGTGA
Enzyme 2 GenBank Gene ID U58766 Link Image
Enzyme 2 GeneCard ID TSTA3 Link Image
Enzyme 2 GenAtlas ID TSTA3 Link Image
Enzyme 2 HGNC ID HGNC:12390 Link Image
Enzyme 2 Chromosome Location 8
Enzyme 2 Locus 8q24.3
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Tonetti M, Sturla L, Bisso A, Benatti U, De Flora A: Synthesis of GDP-L-fucose by the human FX protein. J Biol Chem. 1996 Nov 1;271(44):27274-9. [PubMed Link Image]
  2. Camardella L, Carratore V, Ciardiello MA, Damonte G, Benatti U, De Flora A: Primary structure of human erythrocyte nicotinamide adenine dinucleotide phosphate (NADP[H])-binding protein FX: identification with the mouse tum- transplantation antigen P35B. Blood. 1995 Jan 1;85(1):264-7. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 16520
Enzyme 3 Name cDNA, FLJ94122, Homo sapiens tissue specific transplantation antigen P35B (TSTA3),mRNA (Tissue specific transplantation antigen P35B, isoform CRA_b)
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name TSTA3
Enzyme 3 Protein Sequence >cDNA, FLJ94122, Homo sapiens tissue specific transplantation antigen P35B (TSTA3),mRNA (Tissue specific transplantation antigen P35B, isoform CRA_b) 
MGEPQGSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDTAQTRALFEK
VQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPD
KTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNF
NIEDGHVLPGLIHKVHLAKSSGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPI
ILSVGEEDEVSIKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTP
FKQAVKETCAWFTDNYEQARK
Enzyme 3 Number of Residues 321
Enzyme 3 Molecular Weight 35893
Enzyme 3 Theoretical pI 6.59
Enzyme 3 GO Classification
Function
  • NAD binding
  • binding
  • catalytic activity
  • coenzyme binding
  • cofactor binding
Process
  • cellular metabolism
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • nucleotide-sugar metabolism
  • physiological process
Component
—
Enzyme 3 General Function Cell wall/membrane/envelope biogenesis
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID B2R8Y7 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name B2R8Y7_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 AK313560 Link Image
Enzyme 3 GeneCard ID B2R8Y7 Link Image
Enzyme 3 GenAtlas ID Not Available
Enzyme 3 HGNC ID Not Available
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References Not Available
Enzyme 3 Metabolite References Not Available