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- ChemComp-HF4: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]... -

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Basic information

EntryDatabase: PDB chemical components / ID: HF4
NameName: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one
Synonyms: Cytarabine-TRIPHOSPHATE

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Chemical information

Composition
Formula: C9H16N3O14P3 / Number of atoms: 45 / Formula weight: 483.156 / Formal charge: 0
Others

6dw3

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: HF4 / Ideal coordinates details: Corina / Model coordinates PDB-ID: 6DW3
History
Create componentJun 27, 2018
Modify synonymsJun 27, 2018
Initial releaseOct 10, 2018
Modify synonymsMar 1, 2021
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 12.01C=1N(C(=O)N=C(N)C=1)C2C(C(C(COP(OP(OP(=O)(O)O)(O)=O)(O)=O)O2)O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 2.0.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O

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SMILES CANONICAL

CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2O
OpenEye OEToolkits 2.0.6C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O

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InChI

InChI 1.03InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7+,8-/m1/s1

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InChIKey

InChI 1.03PCDQPRRSZKQHHS-CCXZUQQUSA-N

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SYSTEMATIC NAME

ACDLabs 12.014-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one
OpenEye OEToolkits 2.0.6[[(2~{R},3~{S},4~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

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PDB entries

Showing all 4 items

PDB-6dw3:
SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket

PDB-8k8s:
F8-A22-E4 complex of MPXV in complex with DNA and Ara-CTP

PDB-8v7b:
Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

PDB-9blf:
SARS-CoV-2 core polymerase complex inhibited by araCTP

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