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 ? _pdbx_chem_comp_pcm.first_instance_model_db_code 2OIG #