{"ymdb_id":"YMDB16306","created_at":"2016-09-12T18:34:32.000Z","updated_at":"2016-10-17T22:34:44.000Z","name":"3''-O-acetyl-ADP-ribose","cas":null,"state":null,"melting_point":null,"description":null,"experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":null,"chebi_id":null,"hmdb_id":null,"kegg_id":null,"pubchem_id":null,"cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl ({[(2R,3S,4R)-3-(acetyloxy)-4,5-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphonate","traditional_iupac":"[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl {[(2R,3S,4R)-3-(acetyloxy)-4,5-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphonate","logp":"-6.463762796208627","pka":"3.2634531101801785","alogps_solubility":"5.39e+00 g/l","alogps_logp":"-1.30","alogps_logs":"-2.07","acceptor_count":"15","donor_count":"5","rotatable_bond_count":"11","polar_surface_area":"303.25000000000006","refractivity":"118.03139999999996","polarizability":"50.692156840528924","formal_charge":"-2","physiological_charge":"-2","pka_strongest_basic":"4.996536051873359","pka_strongest_acidic":"1.8569953004136166","bioavailability":"0","number_of_rings":"4","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"1","synonyms":[],"pathways":[{"name":"NAD metabolism","kegg_map_id":null}],"growth_conditions":[],"references":[],"proteins":[{"created_at":"2011-07-22T05:58:28.000Z","updated_at":"2011-07-22T05:58:28.000Z","name":"NAD-dependent histone deacetylase SIR2","uniprot_id":"P06700","uniprot_name":"SIR2_YEAST","enzyme":false,"transporter":false,"gene_name":"SIR2","num_residues":562,"molecular_weight":"63261.30078","theoretical_pi":"8.66","general_function":"Transcription","specific_function":"NAD-dependent deacetylase, which participates in a wide range of cellular events including chromosome silencing, chromosome segregation, DNA recombination and the determination of life span. Involved in transcriptional repression of the silent mating-type loci HML and HMR and telomeric silencing via its association with SIR3 and SIR4. Plays a central role in ribosomal DNA (rDNA) silencing via its association with the RENT complex, preventing hyperrecombination, and repressing transcription from foreign promoters, which contributes to extending life span. Probably represses transcription via the formation of heterochromatin structure, which involves the compaction of chromatin fiber into a more condensed form, although this complex in at least one case can still bind euchromatic levels of positive transcription regulators. Although it displays some NAD-dependent histone deacetylase activity on 'Lys-9' and 'Lys-14' of histone H3 and 'Lys-16' of histone H4 in vitro, such activity is unclear in vivo and may not be essential","reactions":[{"id":1762,"direction":"\u003c\u003e","locations":"nucleus","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2861,"direction":"\u003e","locations":"Cytoplasm. Nucleus;Nucleus, nucleolus.;Nucleus.;Nucleus (Potential);Nucleus","altext":"NAD(+) + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein.","export":false,"pw_reaction_id":null,"source":null},{"id":4196,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006495","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Nucleus, nucleolus.","genbank_gene_id":"X01419","genbank_protein_id":"4470","gene_card_id":"SIR2","chromosome_location":null,"locus":null,"synonyms":["Regulatory protein SIR2","Silent information regulator 2"],"enzyme_classes":[],"go_classes":[{"category":"Function","description":"NAD binding"},{"category":"Function","description":"hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"category":"Function","description":"hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides"},{"category":"Function","description":"nucleotide binding"},{"category":"Function","description":"histone deacetylase activity"},{"category":"Function","description":"NAD-dependent histone deacetylase activity"},{"category":"Function","description":"NAD or NADH binding"},{"category":"Function","description":"hydrolase activity"},{"category":"Function","description":"binding"},{"category":"Function","description":"ion binding"},{"category":"Function","description":"cation binding"},{"category":"Function","description":"metal ion binding"},{"category":"Function","description":"transition metal ion binding"},{"category":"Function","description":"zinc ion binding"},{"category":"Function","description":"catalytic activity"},{"category":"Process","description":"macromolecule metabolic process"},{"category":"Process","description":"macromolecule modification"},{"category":"Process","description":"protein modification process"},{"category":"Process","description":"post-translational protein modification"},{"category":"Process","description":"protein amino acid deacetylation"},{"category":"Process","description":"regulation of transcription, DNA-dependent"},{"category":"Process","description":"biological regulation"},{"category":"Process","description":"metabolic process"},{"category":"Process","description":"regulation of biological process"},{"category":"Process","description":"regulation of metabolic process"},{"category":"Process","description":"regulation of macromolecule metabolic process"},{"category":"Process","description":"regulation of gene expression"},{"category":"Process","description":"regulation of transcription"},{"category":"Process","description":"cellular process"},{"category":"Process","description":"gene silencing"},{"category":"Process","description":"chromatin silencing"}],"pfams":[{"name":"DUF592","identifier":"PF04574"},{"name":"SIR2","identifier":"PF02146"}],"pathways":[{"name":"NAD metabolism","kegg_map_id":null}],"gene_sequence":"ATGACCATCCCACATATGAAATACGCCGTATCAAAGACTAGCGAAAATAAGGTTTCAAATACAGTAAGCCCCACACAAGATAAAGACGCGATCAGAAAACAACCCGATGACATTATAAATAATGATGAACCTTCACATAAGAAGATAAAAGTAGCACAGCCGGATTCCTTGAGGGAAACCAACACAACAGATCCACTTGGGCACACTAAAGCTGCGCTCGGAGAAGTGGCATCGATGGAGCTCAAACCAACTAATGACATGGATCCCTTGGCAGTGTCAGCAGCTTCAGTAGTGTCAATGTCCAATGACGTTTTGAAACCAGAGACGCCCAAGGGGCCAATCATAATCAGTAAAAACCCATCAAATGGTATTTTCTATGGTCCCTCCTTCACTAAACGAGAGTCTCTCAATGCTCGAATGTTTCTGAAATACTATGGTGCACACAAATTTTTAGACACTTACCTCCCCGAGGATTTGAACTCGTTATACATTTACTATCTTATCAAGTTGCTAGGCTTTGAAGTTAAAGATCAAGCGCTTATCGGCACCATCAACAGTATTGTCCATATCAACTCGCAAGAGCGTGTTCAAGATTTGGGAAGTGCAATATCTGTCACAAATGTTGAAGACCCATTGGCAAAAAAGCAAACAGTTCGTCTAATCAAAGATTTGCAAAGAGCAATTAACAAAGTTCTATGTACAAGATTAAGATTATCCAATTTTTTCACTATTGATCATTTTATTCAAAAATTACATACCGCTAGAAAAATTTTGGTCCTGACTGGTGCAGGTGTTTCAACTTCATTAGGGATCCCGGACTTCAGATCTTCTGAGGGGTTCTATTCAAAGATCAAACATTTGGGGCTCGATGATCCCCAAGACGTTTTCAATTACAATATATTTATGCACGACCCCTCTGTTTTCTATAATATTGCCAATATGGTTTTACCTCCAGAAAAAATTTATTCTCCATTGCATAGTTTCATTAAGATGCTACAAATGAAAGGGAAATTATTGAGAAATTATACTCAAAACATTGATAATTTGGAATCTTATGCGGGAATAAGCACAGATAAACTGGTGCAGTGCCATGGCTCTTTTGCTACTGCCACCTGCGTTACCTGCCATTGGAACCTACCCGGTGAGAGGATATTTAATAAAATTAGAAACCTCGAACTTCCACTATGCCCGTACTGTTACAAAAAAAGAAGAGAATATTTCCCAGAGGGATATAATAATAAAGTAGGTGTTGCTGCATCACAGGGTTCAATGTCGGAAAGGCCTCCATATATCCTTAACTCATATGGCGTTCTCAAACCAGATATCACATTCTTTGGCGAAGCACTGCCAAATAAATTTCATAAGAGCATTCGCGAAGATATCTTAGAATGTGATTTGTTGATTTGCATTGGGACAAGTTTAAAAGTAGCGCCAGTGTCTGAAATCGTAAACATGGTTCCTTCCCACGTTCCCCAAGTCCTGATTAATCGTGATCCCGTCAAGCACGCAGAATTTGATTTATCTCTTTTGGGGTACTGTGATGACATTGCAGCTATGGTAGCCCAAAAATGTGGCTGGACGATTCCGCATAAGAAATGGAACGATTTGAAGAACAAGAACTTTAAATGCCAAGAGAAGGATAAGGGCGTGTATGTCGTTACATCAGATGAACATCCCAAAACCCTCTAA","protein_sequence":"MTIPHMKYAVSKTSENKVSNTVSPTQDKDAIRKQPDDIINNDEPSHKKIKVAQPDSLRETNTTDPLGHTKAALGEVASMELKPTNDMDPLAVSAASVVSMSNDVLKPETPKGPIIISKNPSNGIFYGPSFTKRESLNARMFLKYYGAHKFLDTYLPEDLNSLYIYYLIKLLGFEVKDQALIGTINSIVHINSQERVQDLGSAISVTNVEDPLAKKQTVRLIKDLQRAINKVLCTRLRLSNFFTIDHFIQKLHTARKILVLTGAGVSTSLGIPDFRSSEGFYSKIKHLGLDDPQDVFNYNIFMHDPSVFYNIANMVLPPEKIYSPLHSFIKMLQMKGKLLRNYTQNIDNLESYAGISTDKLVQCHGSFATATCVTCHWNLPGERIFNKIRNLELPLCPYCYKKRREYFPEGYNNKVGVAASQGSMSERPPYILNSYGVLKPDITFFGEALPNKFHKSIREDILECDLLICIGTSLKVAPVSEIVNMVPSHVPQVLINRDPVKHAEFDLSLLGYCDDIAAMVAQKCGWTIPHKKWNDLKNKNFKCQEKDKGVYVVTSDEHPKTL"}]}