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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-06-29 00:47:07 UTC
NP-MRD IDNP0000340
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Ribose 5-phosphate
DescriptionD-Ribose 5-phosphate (CAS: 4300-28-1), Also known as R-5-P, belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. D-Ribose 5-phosphate exists in all living species, ranging from bacteria to humans. Within humans, D-ribose 5-phosphate participates in a number of enzymatic reactions. In particular, D-ribose 5-phosphate can be biosynthesized from D-ribulose 5-phosphate; which is mediated by the enzyme ribose-5-phosphate isomerase. In addition, D-ribose 5-phosphate can be biosynthesized from D-ribose; which is catalyzed by the enzyme ribokinase. Outside of the human body, D-ribose 5-phosphate has been detected, but not quantified in cow milk and rices. D-Ribose 5-phosphate is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose 5-phosphate. D-Ribose 5-phosphate is an important intermediate metabolite in the pentose phosphate pathway and in the purine metabolism pathway. The intracellular ribose 5-phosphate concentration is an important determinant of the rate of de novo purine synthesis (PMID: 6699001 ).
Structure
Thumb
Synonyms
ValueSource
5-O-Phosphono-alpha-D-ribofuranoseChEBI
alpha-D-Ribose 5-phosphateChEBI
5-O-Phosphono-a-D-ribofuranoseGenerator
5-O-Phosphono-α-D-ribofuranoseGenerator
a-D-Ribose 5-phosphateGenerator
a-D-Ribose 5-phosphoric acidGenerator
alpha-D-Ribose 5-phosphoric acidGenerator
Α-D-ribose 5-phosphateGenerator
Α-D-ribose 5-phosphoric acidGenerator
D-Ribose 5-phosphoric acidGenerator
D-Ribofuranose 5-phosphateHMDB
R-5-pHMDB
Ribose 5-(dihydrogen phosphate)HMDB
Ribose 5-monophosphateHMDB
Ribose 5-phosphateHMDB
alpha-D-Ribose-5-phosphateHMDB
Α-D-ribose-5-phosphateHMDB
D-Ribose 5-phosphateHMDB
Chemical FormulaC5H11O8P
Average Mass230.1098 Da
Monoisotopic Mass230.01915 Da
IUPAC Name{[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Nameα-D-ribose 5-phosphate
CAS Registry Number3615-55-2
SMILES
OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5?/m1/s1
InChI KeyKTVPXOYAKDPRHY-SOOFDHNKSA-N
Spectra
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
Species
Species of Origin
  • All
  • Chemical Taxonomy
    Description Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
    KingdomOrganic compounds
    Super ClassOrganic oxygen compounds
    ClassOrganooxygen compounds
    Sub ClassCarbohydrates and carbohydrate conjugates
    Direct ParentPentose phosphates
    Alternative Parents
    Substituents
    • Pentose phosphate
    • Pentose-5-phosphate
    • Monosaccharide phosphate
    • Monoalkyl phosphate
    • Alkyl phosphate
    • Phosphoric acid ester
    • Organic phosphoric acid derivative
    • Tetrahydrofuran
    • 1,2-diol
    • Secondary alcohol
    • Hemiacetal
    • Polyol
    • Oxacycle
    • Organoheterocyclic compound
    • Hydrocarbon derivative
    • Organic oxide
    • Alcohol
    • Aliphatic heteromonocyclic compound
    Molecular FrameworkAliphatic heteromonocyclic compounds
    External Descriptors
    Physical Properties
    StateSolid
    Experimental Properties
    PropertyValueReference
    Melting PointNot AvailableNot Available
    Boiling PointNot AvailableNot Available
    Water SolubilityNot AvailableNot Available
    LogPNot AvailableNot Available
    Predicted Properties
    PropertyValueSource
    Water Solubility33.6 g/LALOGPS
    logP-2.1ALOGPS
    logP-2.4ChemAxon
    logS-0.84ALOGPS
    pKa (Strongest Acidic)1.22ChemAxon
    pKa (Strongest Basic)-3.7ChemAxon
    Physiological Charge-2ChemAxon
    Hydrogen Acceptor Count7ChemAxon
    Hydrogen Donor Count5ChemAxon
    Polar Surface Area136.68 ŲChemAxon
    Rotatable Bond Count3ChemAxon
    Refractivity40.83 m³·mol⁻¹ChemAxon
    Polarizability18.25 ųChemAxon
    Number of Rings1ChemAxon
    BioavailabilityYesChemAxon
    Rule of FiveYesChemAxon
    Ghose FilterNoChemAxon
    Veber's RuleNoChemAxon
    MDDR-like RuleNoChemAxon
    HMDB IDHMDB0001548
    DrugBank IDNot Available
    Phenol Explorer Compound IDNot Available
    FoodDB IDFDB001615
    KNApSAcK IDC00007473
    Chemspider ID389102
    KEGG Compound IDC03736
    BioCyc IDCPD-15318
    BiGG IDNot Available
    Wikipedia LinkNot Available
    METLIN IDNot Available
    PubChem Compound440101
    PDB IDNot Available
    ChEBI ID18189
    Good Scents IDNot Available
    References
    General References
    1. Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. [PubMed:15882454 ]
    2. Pilz RB, Willis RC, Boss GR: The influence of ribose 5-phosphate availability on purine synthesis of cultured human lymphoblasts and mitogen-stimulated lymphocytes. J Biol Chem. 1984 Mar 10;259(5):2927-35. [PubMed:6699001 ]
    3. Panosian TD, Nannemann DP, Watkins GR, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM: Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. J Biol Chem. 2011 Mar 11;286(10):8043-8054. doi: 10.1074/jbc.M110.201350. Epub 2010 Dec 30. [PubMed:21193409 ]
    4. Breda A, Martinelli LK, Bizarro CV, Rosado LA, Borges CB, Santos DS, Basso LA: Wild-type phosphoribosylpyrophosphate synthase (PRS) from Mycobacterium tuberculosis: a bacterial class II PRS? PLoS One. 2012;7(6):e39245. doi: 10.1371/journal.pone.0039245. Epub 2012 Jun 20. [PubMed:22745722 ]
    5. Guo L, Zhu Q, Liu H, Zhao J, Lu W, Wang J: Untargeted LC-MS-based metabonomic analysis of the effect of photoperiod on the testes of broiler roosters. J Anim Physiol Anim Nutr (Berl). 2021 Sep 26. doi: 10.1111/jpn.13642. [PubMed:34569089 ]
    6. Rouvinen J, Andberg M, Paakkonen J, Hakulinen N, Koivula A: Current state of and need for enzyme engineering of 2-deoxy-D-ribose 5-phosphate aldolases and its impact. Appl Microbiol Biotechnol. 2021 Aug;105(16-17):6215-6228. doi: 10.1007/s00253-021-11462-0. Epub 2021 Aug 19. [PubMed:34410440 ]