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- ChemComp-56B: 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}me... -

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Basic information

EntryDatabase: PDB chemical components / ID: 56B
NameName: 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one

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Chemical information

Composition
Formula: C17H24N5O10P / Number of atoms: 57 / Formula weight: 489.374 / Formal charge: 0
Others

5d0b

Type: RNA linking / PDB classification: ATOMN / Three letter code: 56B / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5D0B
History
Create componentAug 3, 2015
Initial releaseSep 28, 2016
Other modificationJun 27, 2020
External linksUniChem / ChemSpider / PubChem / ZINC / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

ACDLabs 12.01n2(cc(CNC1C(O)C(O)C=C1)c3c2N=C(N)NC3=O)C4C(O)C(O)C(O4)COP(=O)(O)O
CACTVS 3.385NC1=Nc2n(cc(CN[CH]3C=C[CH](O)[CH]3O)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O
OpenEye OEToolkits 1.9.2c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CNC4C=CC(C4O)O

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SMILES CANONICAL

CACTVS 3.385NC1=Nc2n(cc(CN[C@H]3C=C[C@H](O)[C@@H]3O)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O
OpenEye OEToolkits 1.9.2c1c(c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CN[C@H]4C=C[C@@H]([C@@H]4O)O

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InChI

InChI 1.03InChI=1S/C17H24N5O10P/c18-17-20-14-10(15(27)21-17)6(3-19-7-1-2-8(23)11(7)24)4-22(14)16-13(26)12(25)9(32-16)5-31-33(28,29)30/h1-2,4,7-9,11-13,16,19,23-26H,3,5H2,(H2,28,29,30)(H3,18,20,21,27)/t7-,8-,9+,11+,12+,13+,16+/m0/s1

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InChIKey

InChI 1.03BSABGNSIPKXNDL-AEZJAUAXSA-N

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SYSTEMATIC NAME

ACDLabs 12.012-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
OpenEye OEToolkits 1.9.2[(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

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PDB entries

Showing all 3 items

PDB-7u91:
Crystal structure of queuine salvage enzyme DUF2419, in complex with queuosine-5'-monophosphate

PDB-7ulc:
Crystal structure of queuine salvage enzyme DUF2419 mutant D231N, in complex with queuosine-5'-monophosphate

PDB-9deu:
Crystal structure of epoxyqueuosine reductase QueH in complex with queuosine

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