data_523
# 
_chem_comp.id                                    523 
_chem_comp.name                                  
;2'-DEOXY-5-METHYLCYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H19 N3 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "5-METHYL-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2007-01-22 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        482.191 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     523 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye/OEToolkits V1.4.2" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
523 N1     N1   N 1 1 Y N N N N N 58.736 126.724 57.584 0.359  -3.142 -1.011 N1     523 1  
523 C2     C2   C 0 1 Y N N N N N 57.897 125.955 58.405 -0.661 -3.970 -0.129 C2     523 2  
523 N3     N3   N 0 1 Y N N N N N 57.901 124.621 58.318 -0.352 -5.286 0.121  N3     523 3  
523 C4     C4   C 0 1 Y N N N N N 58.661 123.967 57.439 0.787  -5.920 -0.349 C4     523 4  
523 C5     C5   C 0 1 Y N N N N N 59.523 124.687 56.568 1.668  -5.221 -1.105 C5     523 5  
523 C5A    C5A  C 0 1 N N N N N N 60.366 123.973 55.584 2.947  -5.736 -1.697 C5A    523 6  
523 C6     C6   C 0 1 Y N N N N N 59.544 126.055 56.646 1.394  -3.790 -1.414 C6     523 7  
523 O2     O2   O 0 1 N N N N N N 57.166 126.462 59.235 -1.648 -3.363 0.260  O2     523 8  
523 N4     N4   N 0 1 N N N N N N 58.620 122.598 57.386 0.961  -7.239 -0.017 N4     523 9  
523 "C1'"  C1*  C 0 1 N N R N N N 58.792 128.238 57.641 0.046  -1.732 -1.290 "C1'"  523 10 
523 "C2'"  C2*  C 0 1 N N N N N N 58.475 128.759 59.051 0.643  -0.870 -0.188 "C2'"  523 11 
523 "C3'"  C3*  C 0 1 N N S N N N 59.770 129.466 59.524 1.945  -0.412 -0.806 "C3'"  523 12 
523 "C4'"  C4*  C 0 1 N N R N N N 60.530 129.787 58.174 1.533  -0.203 -2.253 "C4'"  523 13 
523 "O4'"  O4*  O 0 1 N N N N N N 60.121 128.665 57.323 0.546  -1.210 -2.535 "O4'"  523 14 
523 "O3'"  O3*  O 0 1 N N N N N N 59.408 130.698 60.197 2.411  0.778  -0.203 "O3'"  523 15 
523 "C5'"  C5*  C 0 1 N N N N N N 62.082 129.648 58.184 2.685  -0.334 -3.233 "C5'"  523 16 
523 "O5'"  O5*  O 0 1 N N N N N N 62.498 130.927 57.649 2.197  -0.134 -4.549 "O5'"  523 17 
523 PA     PA   P 0 1 N N R N N N 64.116 131.145 57.412 2.346  -1.308 -5.653 PA     523 18 
523 O1A    O1A  O 0 1 N N N N N N 64.710 129.949 56.792 1.535  -0.755 -6.939 O1A    523 19 
523 O2A    O2A  O 0 1 N N N N N N 64.454 132.465 56.543 3.759  -1.725 -5.943 O2A    523 20 
523 O3A    O3A  O 0 1 N N N N N N 64.718 131.360 58.866 1.403  -2.500 -5.106 O3A    523 21 
523 PB     PB   P 0 1 N N S N N N 66.345 131.195 59.003 0.974  -3.910 -5.767 PB     523 22 
523 O1B    O1B  O 0 1 N N N N N N 66.954 131.021 60.349 0.053  -3.493 -7.028 O1B    523 23 
523 O2B    O2B  O 0 1 N N N N N N 66.800 129.941 58.166 2.102  -4.844 -6.092 O2B    523 24 
523 O3B    O3B  O 0 1 N N N N N N 66.907 132.430 58.172 -0.085 -4.469 -4.682 O3B    523 25 
523 PG     PG   P 0 1 N N N N N N 68.145 132.020 57.236 -1.043 -5.770 -4.684 PG     523 26 
523 O1G    O1G  O 0 1 N N N N N N 67.932 132.459 55.801 -2.033 -5.817 -5.810 O1G    523 27 
523 O2G    O2G  O 0 1 N N N N N N 69.435 132.711 57.935 -1.684 -5.771 -3.200 O2G    523 28 
523 O3G    O3G  O 0 1 N N N N N N 68.324 130.444 57.279 0.007  -6.998 -4.641 O3G    523 29 
523 HN3    HN3  H 0 1 N N N N N N 57.314 124.095 58.933 -0.999 -5.828 0.686  HN3    523 30 
523 H5A1   1H5A H 0 0 N N N N N N 59.788 123.796 54.665 3.288  -5.053 -2.471 H5A1   523 31 
523 H5A2   2H5A H 0 0 N N N N N N 61.251 124.583 55.348 2.777  -6.720 -2.128 H5A2   523 32 
523 H5A3   3H5A H 0 0 N N N N N N 60.686 123.009 56.007 3.702  -5.813 -0.918 H5A3   523 33 
523 H6     H6   H 0 1 N N N N N N 60.183 126.622 55.985 2.134  -3.256 -2.033 H6     523 34 
523 HN41   1HN4 H 0 0 N N N N N N 58.610 122.301 56.431 0.311  -7.902 -0.370 HN41   523 35 
523 HN42   2HN4 H 0 0 N N N N N N 59.426 122.223 57.843 1.730  -7.480 0.563  HN42   523 36 
523 "H1'"  H1*  H 0 1 N N N N N N 58.051 128.629 56.929 -1.046 -1.665 -1.298 "H1'"  523 37 
523 "H2'1" 1H2* H 0 0 N N N N N N 57.629 129.462 59.029 0.781  -1.372 0.777  "H2'1" 523 38 
523 "H2'2" 2H2* H 0 0 N N N N N N 58.181 127.946 59.731 0.000  0.000  -0.001 "H2'2" 523 39 
523 "H3'"  H3*  H 0 1 N N N N N N 60.377 128.868 60.220 2.712  -1.189 -0.710 "H3'"  523 40 
523 "H4'"  H4*  H 0 1 N N N N N N 60.297 130.826 57.899 1.064  0.778  -2.394 "H4'"  523 41 
523 "HO3'" HO3* H 0 0 N N N N N N 59.329 130.538 61.130 3.312  0.919  -0.531 "HO3'" 523 42 
523 "H5'1" 1H5* H 0 0 N N N N N N 62.426 128.808 57.563 3.132  -1.330 -3.171 "H5'1" 523 43 
523 "H5'2" 2H5* H 0 0 N N N N N N 62.500 129.427 59.177 3.454  0.417  -3.025 "H5'2" 523 44 
523 HO1A   HO1A H 0 0 N N N N N N 64.838 130.104 55.863 1.971  -0.107 -7.532 HO1A   523 45 
523 HO1B   HO1B H 0 0 N N N N N N 67.900 130.984 60.267 -0.283 -4.197 -7.624 HO1B   523 46 
523 HO2G   HO2G H 0 0 N N N N N N 70.114 132.846 57.284 -2.374 -6.433 -2.981 HO2G   523 47 
523 HO3G   HO3G H 0 0 N N N N N N 68.360 130.105 56.392 -0.330 -7.915 -4.726 HO3G   523 48 
# 
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 
523 N1    C6     DOUB Y N 1  
523 N1    "C1'"  SING N N 2  
523 N1    C2     SING Y N 3  
523 C2    N3     SING Y N 4  
523 C2    O2     DOUB N N 5  
523 N3    C4     SING Y N 6  
523 N3    HN3    SING N N 7  
523 C4    C5     DOUB Y N 8  
523 C4    N4     SING N N 9  
523 C5    C5A    SING N N 10 
523 C5    C6     SING Y N 11 
523 C5A   H5A1   SING N N 12 
523 C5A   H5A2   SING N N 13 
523 C5A   H5A3   SING N N 14 
523 C6    H6     SING N N 15 
523 N4    HN41   SING N N 16 
523 N4    HN42   SING N N 17 
523 "C1'" "O4'"  SING N N 18 
523 "C1'" "C2'"  SING N N 19 
523 "C1'" "H1'"  SING N N 20 
523 "C2'" "C3'"  SING N N 21 
523 "C2'" "H2'1" SING N N 22 
523 "C2'" "H2'2" SING N N 23 
523 "C3'" "C4'"  SING N N 24 
523 "C3'" "O3'"  SING N N 25 
523 "C3'" "H3'"  SING N N 26 
523 "C4'" "O4'"  SING N N 27 
523 "C4'" "C5'"  SING N N 28 
523 "C4'" "H4'"  SING N N 29 
523 "O3'" "HO3'" SING N N 30 
523 "C5'" "O5'"  SING N N 31 
523 "C5'" "H5'1" SING N N 32 
523 "C5'" "H5'2" SING N N 33 
523 "O5'" PA     SING N N 34 
523 PA    O2A    DOUB N N 35 
523 PA    O1A    SING N N 36 
523 PA    O3A    SING N N 37 
523 O1A   HO1A   SING N N 38 
523 O3A   PB     SING N N 39 
523 PB    O2B    DOUB N N 40 
523 PB    O3B    SING N N 41 
523 PB    O1B    SING N N 42 
523 O1B   HO1B   SING N N 43 
523 O3B   PG     SING N N 44 
523 PG    O1G    DOUB N N 45 
523 PG    O3G    SING N N 46 
523 PG    O2G    SING N N 47 
523 O2G   HO2G   SING N N 48 
523 O3G   HO3G   SING N N 49 
# 
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 
523 SMILES           ACDLabs              10.04 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC([N+]=1C(=O)NC(N)=C(C=1)C)CC2O"                                                                                                                       
523 SMILES_CANONICAL CACTVS               3.341 "CC1=C(N)NC(=O)[N+](=C1)[C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2"                                                                                               
523 SMILES           CACTVS               3.341 "CC1=C(N)NC(=O)[N+](=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                       
523 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=C(NC(=O)[N+](=C1)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)N"                                                                                                   
523 SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=C(NC(=O)[N+](=C1)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N"                                                                                                                      
523 InChI            InChI                1.03  "InChI=1S/C10H18N3O13P3/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,14H,2,4H2,1H3,(H6,11,12,15,16,17,18,19,20,21,22)/p+1/t6-,7+,8+/m0/s1" 
523 InChIKey         InChI                1.03  VSWHQKSDLZFLRY-XLPZGREQSA-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 
523 "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5-methylcytidine 5'-(tetrahydrogen triphosphate)
;
523 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-5-methyl-2-oxo-3H-pyrimidin-1-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl (hydroxy-phosphonooxy-phosphoryl) hydrogen 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 
523 "Create component"  2007-01-22 PDBJ 
523 "Modify descriptor" 2011-06-04 RCSB 
523 "Modify synonyms"   2021-03-01 PDBE 
523 "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      523 
_pdbx_chem_comp_synonyms.name         "5-METHYL-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            523 
_pdbx_chem_comp_pcm.modified_residue_id                HIS 
_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               N3 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NE2 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
