data_A1CNT
# 
_chem_comp.id                                    A1CNT 
_chem_comp.name                                  "[(3R,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-08-19 
_chem_comp.pdbx_modified_date                    2025-10-31 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        322.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CNT 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        9Q3C 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
A1CNT O4     O1  O 0 1 N N N N N N 22.299 27.733 57.909 3.722  -2.913 -0.824 O4     A1CNT 1  
A1CNT C6     C1  C 0 1 N N N N N N 21.474 31.185 57.792 2.052  -0.510 1.083  C6     A1CNT 2  
A1CNT "C1'"  C2  C 0 1 N N R N N N 22.536 33.047 56.540 1.625  1.855  0.601  "C1'"  A1CNT 3  
A1CNT C2     C3  C 0 1 N N N N N N 23.329 30.745 56.331 2.843  0.418  -0.935 C2     A1CNT 4  
A1CNT "C2'"  C4  C 0 1 N N R N N N 21.222 33.684 56.079 0.448  2.212  -0.333 "C2'"  A1CNT 5  
A1CNT "C3'"  C5  C 0 1 N N R N N N 21.204 35.072 56.757 -0.802 1.732  0.437  "C3'"  A1CNT 6  
A1CNT C4     C6  C 0 1 N N N N N N 22.292 28.937 57.640 3.247  -1.841 -0.494 C4     A1CNT 7  
A1CNT "C4'"  C7  C 0 1 N N N N N N 22.562 35.128 57.455 -0.232 1.141  1.746  "C4'"  A1CNT 8  
A1CNT C5     C8  C 0 1 N N N N N N 21.369 29.905 58.191 2.569  -1.709 0.741  C5     A1CNT 9  
A1CNT "C5'"  C9  C 0 1 N N N N N N 20.065 35.275 57.737 -1.542 0.655  -0.360 "C5'"  A1CNT 10 
A1CNT C7     C10 C 0 1 N N N N N N 20.324 29.433 59.153 2.426  -2.892 1.664  C7     A1CNT 11 
A1CNT N1     N1  N 0 1 N N N N N N 22.423 31.620 56.895 2.191  0.554  0.234  N1     A1CNT 12 
A1CNT N3     N2  N 0 1 N N N N N N 23.205 29.445 56.740 3.373  -0.765 -1.298 N3     A1CNT 13 
A1CNT O2     O2  O 0 1 N N N N N N 24.172 31.088 55.518 2.964  1.379  -1.670 O2     A1CNT 14 
A1CNT "O2'"  O3  O 0 1 N N N N N N 21.213 33.834 54.668 0.391  3.624  -0.549 "O2'"  A1CNT 15 
A1CNT "O4'"  O4  O 0 1 N N N N N N 22.934 33.763 57.697 1.043  1.795  1.921  "O4'"  A1CNT 16 
A1CNT "O5'"  O5  O 0 1 N N N N N N 19.931 34.099 58.544 -2.755 0.314  0.313  "O5'"  A1CNT 17 
A1CNT OP1    O6  O 0 1 N N N N N N 17.703 34.986 59.341 -3.073 -2.068 -0.461 OP1    A1CNT 18 
A1CNT OP2    O7  O 0 1 N N N N N N 18.343 32.527 59.648 -4.968 -1.009 0.827  OP2    A1CNT 19 
A1CNT P      P1  P 0 1 N N N N N N 18.927 34.026 59.810 -3.787 -0.789 -0.244 P      A1CNT 20 
A1CNT H6     H1  H 0 1 N N N N N N 20.780 31.907 58.195 1.528  -0.391 2.019  H6     A1CNT 21 
A1CNT "H1'"  H2  H 0 1 N N N N N N 23.284 33.167 55.743 2.392  2.629  0.559  "H1'"  A1CNT 22 
A1CNT "H2'"  H3  H 0 1 N N N N N N 20.369 33.085 56.430 0.539  1.683  -1.282 "H2'"  A1CNT 23 
A1CNT "H3'"  H4  H 0 1 N N N N N N 21.162 35.850 55.981 -1.464 2.571  0.653  "H3'"  A1CNT 24 
A1CNT "H4'"  H5  H 0 1 N N N N N N 23.305 35.619 56.809 -0.893 1.366  2.583  "H4'"  A1CNT 25 
A1CNT "H4''" H6  H 0 0 N N N N N N 22.482 35.677 58.405 -0.096 0.064  1.648  "H4''" A1CNT 26 
A1CNT "H5'"  H7  H 0 1 N N N N N N 20.281 36.141 58.380 -1.773 1.035  -1.355 "H5'"  A1CNT 27 
A1CNT "H5''" H8  H 0 0 N N N N N N 19.130 35.452 57.185 -0.912 -0.230 -0.446 "H5''" A1CNT 28 
A1CNT H73    H9  H 0 1 N N N N N N 19.709 30.286 59.475 2.906  -3.763 1.215  H73    A1CNT 29 
A1CNT H71    H10 H 0 1 N N N N N N 19.684 28.685 58.662 2.901  -2.668 2.619  H71    A1CNT 30 
A1CNT H72    H11 H 0 1 N N N N N N 20.810 28.980 60.030 1.369  -3.103 1.824  H72    A1CNT 31 
A1CNT H3     H12 H 0 1 N N N N N N 23.848 28.791 56.342 3.847  -0.845 -2.141 H3     A1CNT 32 
A1CNT H1     H13 H 0 1 N N N N N N 20.393 34.230 54.396 1.179  3.988  -0.976 H1     A1CNT 33 
A1CNT HP     H14 H 0 1 N N N N N N 17.450 32.568 59.327 -5.628 -1.662 0.556  HP     A1CNT 34 
A1CNT OP3    OP3 O 0 1 N Y N N N N 19.612 34.446 61.143 -4.413 -0.282 -1.638 OP3    A1CNT 35 
A1CNT H2     H15 H 0 1 N Y N N N N 19.190 35.226 61.484 -4.897 0.553  -1.571 H2     A1CNT 36 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
A1CNT C4    C5     SING N N 1  
A1CNT C5    C6     DOUB N N 2  
A1CNT C6    N1     SING N N 3  
A1CNT N1    C2     SING N N 4  
A1CNT C4    N3     SING N N 5  
A1CNT C2    N3     SING N N 6  
A1CNT C2    O2     DOUB N N 7  
A1CNT N1    "C1'"  SING N N 8  
A1CNT "C1'" "C2'"  SING N N 9  
A1CNT "C2'" "C3'"  SING N N 10 
A1CNT "C3'" "C4'"  SING N N 11 
A1CNT "C1'" "O4'"  SING N N 12 
A1CNT "C4'" "O4'"  SING N N 13 
A1CNT "C3'" "C5'"  SING N N 14 
A1CNT "C5'" "O5'"  SING N N 15 
A1CNT "O5'" P      SING N N 16 
A1CNT P     OP2    SING N N 17 
A1CNT P     OP1    DOUB N N 18 
A1CNT "C2'" "O2'"  SING N N 19 
A1CNT C5    C7     SING N N 20 
A1CNT C4    O4     DOUB N N 21 
A1CNT C6    H6     SING N N 22 
A1CNT "C1'" "H1'"  SING N N 23 
A1CNT "C2'" "H2'"  SING N N 24 
A1CNT "C3'" "H3'"  SING N N 25 
A1CNT "C4'" "H4'"  SING N N 26 
A1CNT "C4'" "H4''" SING N N 27 
A1CNT "C5'" "H5'"  SING N N 28 
A1CNT "C5'" "H5''" SING N N 29 
A1CNT C7    H73    SING N N 30 
A1CNT C7    H71    SING N N 31 
A1CNT C7    H72    SING N N 32 
A1CNT N3    H3     SING N N 33 
A1CNT "O2'" H1     SING N N 34 
A1CNT OP2   HP     SING N N 35 
A1CNT P     OP3    SING N N 36 
A1CNT OP3   H2     SING N N 37 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
A1CNT SMILES           ACDLabs              14.52   "O=P(O)(O)OCC1COC(N2C=C(C)C(=O)NC2=O)C1O"                                                                                                          
A1CNT InChI            InChI                1.06    "InChI=1S/C10H15N2O8P/c1-5-2-12(10(15)11-8(5)14)9-7(13)6(3-19-9)4-20-21(16,17)18/h2,6-7,9,13H,3-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7-,9-/m1/s1" 
A1CNT InChIKey         InChI                1.06    CLFGYSCORDJBPE-ZXFLCMHBSA-N                                                                                                                        
A1CNT SMILES_CANONICAL CACTVS               3.385   "CC1=CN([C@@H]2OC[C@H](CO[P](O)(O)=O)[C@H]2O)C(=O)NC1=O"                                                                                           
A1CNT SMILES           CACTVS               3.385   "CC1=CN([CH]2OC[CH](CO[P](O)(O)=O)[CH]2O)C(=O)NC1=O"                                                                                               
A1CNT SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H](CO2)COP(=O)(O)O)O"                                                                                           
A1CNT SMILES           "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)C2C(C(CO2)COP(=O)(O)O)O"                                                                                                        
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
A1CNT "SYSTEMATIC NAME" ACDLabs              14.52   "[(3R,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl]methyl dihydrogen phosphate"         
A1CNT "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(3~{R},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1CNT "Create component"  2025-08-19 RCSB 
A1CNT "Modify descriptor" 2025-10-30 RCSB 
A1CNT "Initial release"   2025-11-05 RCSB 
# 
