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- ChemComp-XC5: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]m... -

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Basic information

EntryDatabase: PDB chemical components / ID: XC5
NameName: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine

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Chemical information

Composition
Formula: C10H18N3O12P3 / Number of atoms: 46 / Formula weight: 465.184 / Formal charge: 0
Others

5v1p

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: XC5 / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5V1P
History
Create componentMar 6, 2017
Initial releaseMay 10, 2017
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 12.01P(=O)(O)(CP(O)(OP(=O)(O)O)=O)OCC2C(CC(N1C=CC(=NC1=O)N)O2)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 2.0.6C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O

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SMILES CANONICAL

CACTVS 3.385NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 2.0.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O

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InChI

InChI 1.03InChI=1S/C10H18N3O12P3/c11-8-1-2-13(10(15)12-8)9-3-6(14)7(24-9)4-23-26(16,17)5-27(18,19)25-28(20,21)22/h1-2,6-7,9,14H,3-5H2,(H,16,17)(H,18,19)(H2,11,12,15)(H2,20,21,22)/t6-,7+,9+/m0/s1

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InChIKey

InChI 1.03YSCOIIOUWFAHFY-LKEWCRSYSA-N

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SYSTEMATIC NAME

ACDLabs 12.012'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
OpenEye OEToolkits 2.0.6[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid

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PDB entries

Showing all 4 items

PDB-5v1p:
DNA polymerase beta substrate complex with 8-oxoG:C at the primer terminus and incoming dCTP analog

PDB-5vez:
DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP analog

PDB-6go5:
TdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped DNA substrate

PDB-7s9p:
Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog

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