A1L9Q

4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-3-methoxy-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2-thione

Created:	2025-05-20
Last modified:	2025-11-12

Find Related PDB Entry
1 entries where A1L9Q is found in a polymer sequence

Find related ligands:

Similar Ligands (Stereospecific) Similar Ligands (including Stereoisomers) Similar Ligands (Quick Screen) Similar Ligands (Substructure Stereospecific) Similar Ligands (Substructure including Stereoisomers)

Chemical Details
Formal Charge	0
Atom Count	38
Chiral Atom Count	4
Bond Count	39
Aromatic Bond Count	0

2D diagram of A1L9Q

Toggle Hydrogen Toggle Labels

Chemical Component Summary
Name	4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-3-methoxy-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2-thione
Systematic Name (OpenEye OEToolkits)	[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-sulfanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
Formula	C₁₀ H₁₆ N₃ O₇ P S
Molecular Weight	353.289
Type	RNA LINKING

Chemical Descriptors
Type	Program	Version	Descriptor
SMILES	CACTVS	3.385	CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=S)N
SMILES	OpenEye OEToolkits	2.0.7	COC1C(C(OC1N2C=CC(=NC2=S)N)COP(=O)(O)O)O
Canonical SMILES	CACTVS	3.385	CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=S)N
Canonical SMILES	OpenEye OEToolkits	2.0.7	CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=S)N)COP(=O)(O)O)O
InChI	InChI	1.06	InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(15,16)17)20-9(8)13-3-2-6(11)12-10(13)22/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,22)(H2,15,16,17)/t5-,7-,8-,9-/m1/s1
InChIKey	InChI	1.06	GWFOPAUVJXMOAL-ZOQUXTDFSA-N

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.