data_A1CZ2
# 
_chem_comp.id                                    A1CZ2 
_chem_comp.name                                  
;5-methyl-5,6-dihydrocytidine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H18 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-11-06 
_chem_comp.pdbx_modified_date                    2026-05-29 
_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                        339.239 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     A1CZ2 
_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        9Z2N 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
A1CZ2 "C1'"  C1  C 0 1 N N R N N N 121.582 115.242 130.131 1.187  -1.070 -0.670 "C1'"  A1CZ2 1  
A1CZ2 C2     C2  C 0 1 N N N N N N 119.450 116.560 130.572 2.451  0.232  0.948  C2     A1CZ2 2  
A1CZ2 "C2'"  C3  C 0 1 N N R N N N 120.931 114.270 129.138 1.039  -2.315 0.232  "C2'"  A1CZ2 3  
A1CZ2 "C3'"  C4  C 0 1 N N S N N N 121.218 114.945 127.796 -0.487 -2.450 0.438  "C3'"  A1CZ2 4  
A1CZ2 C4     C5  C 0 1 N N N N N N 119.155 117.582 132.633 4.280  1.541  0.412  C4     A1CZ2 5  
A1CZ2 "C4'"  C6  C 0 1 N N R N N N 122.532 115.663 128.043 -1.080 -1.271 -0.364 "C4'"  A1CZ2 6  
A1CZ2 C5     C7  C 0 1 N N R N N N 120.630 117.577 132.916 4.062  1.283  -1.057 C5     A1CZ2 7  
A1CZ2 "C5'"  C8  C 0 1 N N N N N N 122.794 116.851 127.156 -2.287 -0.682 0.369  "C5'"  A1CZ2 8  
A1CZ2 C6     C9  C 0 1 N N N N N N 121.210 116.298 132.301 3.463  -0.111 -1.243 C6     A1CZ2 9  
A1CZ2 CM5    C10 C 0 1 N N N N N N 121.213 118.857 132.338 3.100  2.332  -1.618 CM5    A1CZ2 10 
A1CZ2 N1     N1  N 0 1 N N N N N N 120.647 116.056 130.964 2.371  -0.299 -0.284 N1     A1CZ2 11 
A1CZ2 N3     N2  N 0 1 N N N N N N 118.704 117.324 131.420 3.472  1.028  1.302  N3     A1CZ2 12 
A1CZ2 N4     N3  N 0 1 N N N N N N 118.397 118.327 133.419 5.319  2.307  0.812  N4     A1CZ2 13 
A1CZ2 O2     O1  O 0 1 N N N N N N 119.009 116.345 129.466 1.576  -0.010 1.759  O2     A1CZ2 14 
A1CZ2 "O2'"  O2  O 0 1 N N N N N N 121.629 113.040 129.220 1.560  -3.473 -0.424 "O2'"  A1CZ2 15 
A1CZ2 "O3'"  O3  O 0 1 N N N N N N 121.277 114.041 126.706 -0.954 -3.696 -0.084 "O3'"  A1CZ2 16 
A1CZ2 "O4'"  O4  O 0 1 N N N N N N 122.418 116.115 129.408 -0.013 -0.300 -0.436 "O4'"  A1CZ2 17 
A1CZ2 "O5'"  O5  O 0 1 N N N N N N 123.945 117.572 127.571 -2.890 0.329  -0.441 "O5'"  A1CZ2 18 
A1CZ2 OP1    O6  O 0 1 N N N N N N 126.336 118.203 127.097 -4.512 2.298  -1.076 OP1    A1CZ2 19 
A1CZ2 OP2    O7  O 0 1 N N N N N N 125.281 115.979 126.188 -5.447 0.167  0.147  OP2    A1CZ2 20 
A1CZ2 P      P1  P 0 1 N N N N N N 125.407 117.018 127.285 -4.188 1.162  0.018  P      A1CZ2 21 
A1CZ2 OP3    O8  O 0 1 N N N N N N 125.818 116.241 128.626 -3.927 1.800  1.328  OP3    A1CZ2 22 
A1CZ2 "H1'"  H1  H 0 1 N N N N N N 122.202 114.642 130.814 1.250  -1.365 -1.717 "H1'"  A1CZ2 23 
A1CZ2 "H2'"  H2  H 0 1 N N N N N N 119.850 114.172 129.319 1.543  -2.158 1.186  "H2'"  A1CZ2 24 
A1CZ2 "H3'"  H3  H 0 1 N N N N N N 120.438 115.699 127.614 -0.739 -2.362 1.495  "H3'"  A1CZ2 25 
A1CZ2 "H4'"  H4  H 0 1 N N N N N N 123.360 114.946 127.947 -1.366 -1.597 -1.363 "H4'"  A1CZ2 26 
A1CZ2 H4     H5  H 0 1 N N N N N N 120.796 117.561 134.003 5.015  1.344  -1.583 H4     A1CZ2 27 
A1CZ2 "H5'"  H6  H 0 1 N N N N N N 122.946 116.499 126.125 -3.013 -1.471 0.566  "H5'"  A1CZ2 28 
A1CZ2 "H5''" H7  H 0 0 N N N N N N 121.922 117.521 127.190 -1.961 -0.244 1.313  "H5''" A1CZ2 29 
A1CZ2 H5     H8  H 0 1 N N N N N N 122.302 116.401 132.219 3.079  -0.209 -2.259 H5     A1CZ2 30 
A1CZ2 H6     H9  H 0 1 N N N N N N 120.971 115.445 132.952 4.232  -0.863 -1.069 H6     A1CZ2 31 
A1CZ2 HM51   H10 H 0 0 N N N N N N 120.749 119.726 132.828 2.148  2.272  -1.089 HM51   A1CZ2 32 
A1CZ2 HM52   H11 H 0 0 N N N N N N 122.299 118.876 132.511 3.527  3.326  -1.485 HM52   A1CZ2 33 
A1CZ2 HM53   H12 H 0 0 N N N N N N 121.013 118.895 131.257 2.938  2.146  -2.680 HM53   A1CZ2 34 
A1CZ2 HN41   H13 H 0 0 N N N N N N 117.519 118.671 133.087 5.921  2.689  0.155  HN41   A1CZ2 35 
A1CZ2 HN42   H14 H 0 0 N N N N N N 118.702 118.546 134.346 5.462  2.475  1.757  HN42   A1CZ2 36 
A1CZ2 "HO2'" H15 H 0 0 N N N N N N 121.446 112.627 130.056 1.492  -4.284 0.098  "HO2'" A1CZ2 37 
A1CZ2 "HO3'" H16 H 0 0 N N N N N N 120.432 113.621 126.596 -0.567 -4.472 0.344  "HO3'" A1CZ2 38 
A1CZ2 H1     H17 H 0 1 N N N N N N 126.961 118.232 127.812 -5.284 2.840  -0.864 H1     A1CZ2 39 
A1CZ2 H2     H18 H 0 1 N N N N N N 125.472 115.119 126.543 -5.676 -0.287 -0.676 H2     A1CZ2 40 
# 
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 
A1CZ2 CM5   C5     SING N N 1  
A1CZ2 C5    C6     SING N N 2  
A1CZ2 C6    N1     SING N N 3  
A1CZ2 N1    "C1'"  SING N N 4  
A1CZ2 "C1'" "O4'"  SING N N 5  
A1CZ2 "O4'" "C4'"  SING N N 6  
A1CZ2 "C4'" "C5'"  SING N N 7  
A1CZ2 "C5'" "O5'"  SING N N 8  
A1CZ2 "O5'" P      SING N N 9  
A1CZ2 P     OP3    DOUB N N 10 
A1CZ2 P     OP1    SING N N 11 
A1CZ2 P     OP2    SING N N 12 
A1CZ2 "C4'" "C3'"  SING N N 13 
A1CZ2 "C3'" "O3'"  SING N N 14 
A1CZ2 "C3'" "C2'"  SING N N 15 
A1CZ2 "C2'" "O2'"  SING N N 16 
A1CZ2 N1    C2     SING N N 17 
A1CZ2 C2    O2     DOUB N N 18 
A1CZ2 C2    N3     SING N N 19 
A1CZ2 N3    C4     DOUB N N 20 
A1CZ2 C4    N4     SING N N 21 
A1CZ2 C5    C4     SING N N 22 
A1CZ2 "C1'" "C2'"  SING N N 23 
A1CZ2 "C1'" "H1'"  SING N N 24 
A1CZ2 "C2'" "H2'"  SING N N 25 
A1CZ2 "C3'" "H3'"  SING N N 26 
A1CZ2 "C4'" "H4'"  SING N N 27 
A1CZ2 C5    H4     SING N N 28 
A1CZ2 "C5'" "H5'"  SING N N 29 
A1CZ2 "C5'" "H5''" SING N N 30 
A1CZ2 C6    H5     SING N N 31 
A1CZ2 C6    H6     SING N N 32 
A1CZ2 CM5   HM51   SING N N 33 
A1CZ2 CM5   HM52   SING N N 34 
A1CZ2 CM5   HM53   SING N N 35 
A1CZ2 N4    HN41   SING N N 36 
A1CZ2 N4    HN42   SING N N 37 
A1CZ2 "O2'" "HO2'" SING N N 38 
A1CZ2 "O3'" "HO3'" SING N N 39 
A1CZ2 OP1   H1     SING N N 40 
A1CZ2 OP2   H2     SING N N 41 
# 
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 
A1CZ2 SMILES           ACDLabs              14.52   "O=P(O)(O)OCC1OC(N2CC(C)C(N)=NC2=O)C(O)C1O"                                                                                                                   
A1CZ2 InChI            InChI                1.06    "InChI=1S/C10H18N3O8P/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(21-9)3-20-22(17,18)19/h4-7,9,14-15H,2-3H2,1H3,(H2,11,12,16)(H2,17,18,19)/t4-,5-,6-,7-,9-/m1/s1" 
A1CZ2 InChIKey         InChI                1.06    UPMDOPXGFUWFLX-DMKSXPFUSA-N                                                                                                                                   
A1CZ2 SMILES_CANONICAL CACTVS               3.385   "C[C@@H]1CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N"                                                                                          
A1CZ2 SMILES           CACTVS               3.385   "C[CH]1CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N"                                                                                                  
A1CZ2 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@@H]1CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                          
A1CZ2 SMILES           "OpenEye OEToolkits" 3.1.0.0 "CC1CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(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 
A1CZ2 "SYSTEMATIC NAME" ACDLabs              14.52   
;5-methyl-5,6-dihydrocytidine 5'-(dihydrogen phosphate)
;
A1CZ2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{S},4~{R},5~{R})-5-[(5~{R})-6-azanyl-5-methyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl]-3,4-bis(oxidanyl)oxolan-2-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 
A1CZ2 "Create component" 2025-11-06 RCSB 
A1CZ2 "Initial release"  2026-06-03 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1CZ2 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C6 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
