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- ChemComp-N5P: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]... -

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Basic information

EntryDatabase: PDB chemical components / ID: N5P
NameName: 1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro
Synonyms: 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE

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Chemical information

Composition
Formula: C13H17N2O14P3 / Number of atoms: 49 / Formula weight: 518.2 / Formal charge: 0
OthersType: NON-POLYMER / PDB classification: HETAIN / Three letter code: N5P / Ideal coordinates details: Corina
History
Create componentMar 21, 2007
Modify descriptorJun 4, 2011
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / 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 12.01[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
OpenEye OEToolkits 1.7.2c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]

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SMILES CANONICAL

CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
OpenEye OEToolkits 1.7.2c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]

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InChI

InChI 1.03InChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1

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InChIKey

InChI 1.03JJJBDAFRCKSXDR-YNEHKIRRSA-N

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SYSTEMATIC NAME

ACDLabs 12.011-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole
OpenEye OEToolkits 1.7.2[[5-(5-nitroindol-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

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PDB entries

Showing all 4 items

PDB-2oyq:
Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog

PDB-2ozm:
Crystal structure of RB69 gp43 in complex with DNA with 5-NITP opposite an abasic site analog

PDB-3rsr:
Crystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Reductase

PDB-3t3f:
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP

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