ChemComp-VT7: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]ox...

Basic information

• Entry: Database: PDB chemical components / ID: VT7
• Name: Name: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

Chemical information

Composition

Formula: C₁₁H₁₇F₂N₂O₁₃P₃ / Number of atoms: 48 / Formula weight: 516.176 / Formal charge: 0

Others

6cto

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: VT7 / Ideal coordinates details: Corina / Model coordinates PDB-ID: 6CTO

History

Create component	Mar 26, 2018
Initial release	Jun 20, 2018

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Details

SMILES

• ACDLabs 12.01: O=C1C(C)=CN(C(N1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(F)(P(O)(O)=O)F)=O
• CACTVS 3.385: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O
• OpenEye OEToolkits 2.0.6: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O

SMILES CANONICAL

• CACTVS 3.385: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O
• OpenEye OEToolkits 2.0.6: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O

InChI

• InChI 1.03: InChI=1S/C11H17F2N2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-31(24,25)28-30(22,23)11(12,13)29(19,20)21/h3,6-8,16H,2,4H2,1H3,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t6-,7+,8+/m0/s1

InChIKey

• InChI 1.03: PZJVGXNXDJKXPK-XLPZGREQSA-N

SYSTEMATIC NAME

• ACDLabs 12.01: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine
• OpenEye OEToolkits 2.0.6: [bis(fluoranyl)-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid

PDB entries

Showing all 1 items

PDB-6cto:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue