5DB

1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one

Created:	2015-09-08
Last modified:	2016-08-10

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2 entries where 5DB is found in a polymer sequence

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Chemical Details
Formal Charge	0
Atom Count	39
Chiral Atom Count	3
Bond Count	40
Aromatic Bond Count	0

2D diagram of 5DB

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Chemical Component Summary
Name	1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one
Systematic Name (OpenEye OEToolkits)	[(2R,3S,5R)-5-(4-methoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
Formula	C₁₁ H₁₇ N₂ O₈ P
Molecular Weight	336.235
Type	DNA LINKING

Chemical Descriptors
Type	Program	Version	Descriptor
SMILES	ACDLabs	12.01	P(O)(O)(OCC1OC(CC1O)N2C(N=C(C(=C2)C)OC)=O)=O
SMILES	CACTVS	3.385	COC1=NC(=O)N(C=C1C)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
SMILES	OpenEye OEToolkits	1.9.2	CC1=CN(C(=O)N=C1OC)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES	CACTVS	3.385	COC1=NC(=O)N(C=C1C)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
Canonical SMILES	OpenEye OEToolkits	1.9.2	CC1=CN(C(=O)N=C1OC)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
InChI	InChI	1.03	InChI=1S/C11H17N2O8P/c1-6-4-13(11(15)12-10(6)19-2)9-3-7(14)8(21-9)5-20-22(16,17)18/h4,7-9,14H,3,5H2,1-2H3,(H2,16,17,18)/t7-,8+,9+/m0/s1
InChIKey	InChI	1.03	ZEXYXJZBCLRLBU-DJLDLDEBSA-N

Related Resource References

Resource Name	Reference
PubChem	137348339

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.