ChemComp-DPB: (S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHONO)BENZYLIDENE-B-D-THREO-PENTOF...

Basic information

• Entry: Database: PDB chemical components / ID: DPB
• Name: Name: (S)-1-[2'-deoxy-3',5'-O-(1-phosphono)benzylidene-B-D-threo-pentofuranosyl]thymine; Synonyms: DPB-T

Chemical information

Composition

Formula: C₁₇H₁₉N₂O₈P / Number of atoms: 47 / Formula weight: 410.315 / Formal charge: 0

Others

DT

Type: DNA LINKING / PDB classification: ATOMN / One letter code: T / Three letter code: DPB / Parent comp.: DT

History

Create component	Sep 17, 2003
Modify descriptor	Jun 4, 2011
Modify synonyms	Jun 5, 2020

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Details

SMILES

• ACDLabs 10.04: O=C1C(=CN(C(=O)N1)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4)C
• CACTVS 3.341: CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
• OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccccc4)P(=O)(O)O

SMILES CANONICAL

• CACTVS 3.341: CC1=CN([C@@H]2C[C@@H]3O[C@@](OC[C@@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
• OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]3[C@@H](O2)CO[C@](O3)(c4ccccc4)P(=O)(O)O

InChI

• InChI 1.03: InChI=1S/C17H19N2O8P/c1-10-8-19(16(21)18-15(10)20)14-7-12-13(26-14)9-25-17(27-12,28(22,23)24)11-5-3-2-4-6-11/h2-6,8,12-14H,7,9H2,1H3,(H,18,20,21)(H2,22,23,24)/t12-,13-,14-,17-/m0/s1

InChIKey

• InChI 1.03: WTZFKHNHHRPQOU-WSMBLCCSSA-N

SYSTEMATIC NAME

• ACDLabs 10.04: 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-L-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
• OpenEye OEToolkits 1.5.0: [(2S,4aS,6S,7aS)-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2-phenyl-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid

PDB entries

Showing all 1 items

PDB-1q91:
Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T