data_U48 # _chem_comp.id U48 _chem_comp.name "5-METHYL-2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2021-01-20 _chem_comp.pdbx_modified_date 2021-11-05 _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 322.232 _chem_comp.one_letter_code C _chem_comp.three_letter_code U48 _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 7BL0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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.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 U48 C2 C1 C 0 1 N N N 39.054 32.744 39.371 -2.279 0.146 -0.839 C2 U48 1 U48 O2 O1 O 0 1 N N N 38.761 32.016 38.437 -1.328 -0.090 -1.565 O2 U48 2 U48 C4 C2 C 0 1 N N N 40.570 34.448 40.264 -4.339 1.147 -0.534 C4 U48 3 U48 C5 C3 C 0 1 N N N 39.864 34.534 41.524 -4.373 0.667 0.792 C5 U48 4 U48 C6 C4 C 0 1 N N N 38.717 33.667 41.613 -3.336 -0.074 1.248 C6 U48 5 U48 OP1 O2 O 0 1 N N N 32.317 32.109 44.323 5.278 0.111 -0.449 OP1 U48 6 U48 P P1 P 0 1 N N N 32.814 33.439 43.834 4.246 1.020 0.097 P U48 7 U48 OP2 O3 O 0 1 N N N 32.268 34.597 44.612 3.817 2.085 -1.033 OP2 U48 8 U48 "O5'" O4 O 0 1 N N N 34.453 33.466 43.747 2.957 0.164 0.543 "O5'" U48 9 U48 "C5'" C5 C 0 1 N N N 35.188 32.232 43.611 2.267 -0.721 -0.341 "C5'" U48 10 U48 "C4'" C6 C 0 1 N N R 35.207 31.760 42.135 1.097 -1.372 0.400 "C4'" U48 11 U48 "O4'" O5 O 0 1 N N N 36.053 32.677 41.391 0.076 -0.394 0.696 "O4'" U48 12 U48 "C3'" C7 C 0 1 N N S 35.866 30.367 41.966 0.371 -2.392 -0.514 "C3'" U48 13 U48 "O3'" O6 O 0 1 N N N 35.192 29.613 40.956 0.999 -3.674 -0.446 "O3'" U48 14 U48 "C2'" C8 C 0 1 N N N 37.291 30.687 41.500 -1.045 -2.436 0.110 "C2'" U48 15 U48 "C1'" C9 C 0 1 N N R 37.102 31.979 40.696 -1.148 -1.117 0.907 "C1'" U48 16 U48 N1 N1 N 0 1 N N N 38.313 32.817 40.552 -2.283 -0.327 0.421 N1 U48 17 U48 C5M C10 C 0 1 N N N 40.279 35.462 42.651 -5.546 0.974 1.686 C5M U48 18 U48 N4 N2 N 0 1 N N N 41.650 35.224 39.978 -5.379 1.902 -1.023 N4 U48 19 U48 N3 N3 N 1 1 N N N 40.159 33.573 39.280 -3.295 0.871 -1.304 N3 U48 20 U48 O1 O7 O 0 1 N Y N 32.483 33.616 42.242 4.839 1.801 1.373 O1 U48 21 U48 H6 H2 H 0 1 N N N 38.140 33.664 42.526 -3.339 -0.453 2.260 H1 U48 22 U48 H2 H3 H 0 1 N N N 31.690 34.276 45.294 3.142 2.714 -0.744 H2 U48 23 U48 "H5'" H4 H 0 1 N N N 34.711 31.458 44.230 1.889 -0.160 -1.195 "H5'" U48 24 U48 "H5''" H5 H 0 0 N N N 36.222 32.389 43.952 2.952 -1.495 -0.688 "H5''" U48 25 U48 "H4'" H6 H 0 1 N N N 34.183 31.743 41.733 1.443 -1.854 1.314 "H4'" U48 26 U48 "H3'" H7 H 0 1 N N N 35.887 29.838 42.930 0.333 -2.034 -1.543 "H3'" U48 27 U48 H3T H8 H 0 1 N N N 34.309 29.415 41.245 0.581 -4.346 -1.001 H3T U48 28 U48 "H2'" H9 H 0 1 N N N 37.691 29.881 40.867 -1.805 -2.472 -0.671 "H2'" U48 29 U48 "H2''" H10 H 0 0 N N N 37.962 30.848 42.357 -1.143 -3.293 0.775 "H2''" U48 30 U48 "H1'" H11 H 0 1 N N N 36.747 31.703 39.692 -1.273 -1.335 1.967 "H1'" U48 31 U48 H53 H12 H 0 1 N N N 39.587 35.343 43.498 -6.272 1.577 1.140 H53 U48 32 U48 H51 H13 H 0 1 N N N 41.300 35.212 42.974 -6.015 0.042 2.004 H51 U48 33 U48 H52 H14 H 0 1 N N N 40.250 36.503 42.298 -5.202 1.524 2.562 H52 U48 34 U48 H41 H15 H 0 1 N N N 41.983 35.884 40.651 -6.139 2.106 -0.456 H41 U48 35 U48 H42 H16 H 0 1 N N N 42.111 35.134 39.095 -5.352 2.231 -1.935 H42 U48 36 U48 H3 H17 H 0 1 N N N 40.699 33.535 38.439 -3.270 1.201 -2.216 H3 U48 37 U48 H4 H18 H 0 1 N N N 32.036 32.841 41.923 5.619 2.339 1.177 H4 U48 38 # # 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 U48 O2 C2 DOUB N N 1 U48 N3 C2 SING N N 2 U48 N3 C4 DOUB N N 3 U48 C2 N1 SING N N 4 U48 N4 C4 SING N N 5 U48 C4 C5 SING N N 6 U48 N1 "C1'" SING N N 7 U48 N1 C6 SING N N 8 U48 "C1'" "O4'" SING N N 9 U48 "C1'" "C2'" SING N N 10 U48 "O3'" "C3'" SING N N 11 U48 "O4'" "C4'" SING N N 12 U48 "C2'" "C3'" SING N N 13 U48 C5 C6 DOUB N N 14 U48 C5 C5M SING N N 15 U48 "C3'" "C4'" SING N N 16 U48 "C4'" "C5'" SING N N 17 U48 "C5'" "O5'" SING N N 18 U48 "O5'" P SING N N 19 U48 P OP1 DOUB N N 20 U48 P OP2 SING N N 21 U48 P O1 SING N N 22 U48 C6 H6 SING N N 23 U48 OP2 H2 SING N N 24 U48 "C5'" "H5'" SING N N 25 U48 "C5'" "H5''" SING N N 26 U48 "C4'" "H4'" SING N N 27 U48 "C3'" "H3'" SING N N 28 U48 "O3'" H3T SING N N 29 U48 "C2'" "H2'" SING N N 30 U48 "C2'" "H2''" SING N N 31 U48 "C1'" "H1'" SING N N 32 U48 C5M H53 SING N N 33 U48 C5M H51 SING N N 34 U48 C5M H52 SING N N 35 U48 N4 H41 SING N N 36 U48 N4 H42 SING N N 37 U48 N3 H3 SING N N 38 U48 O1 H4 SING N N 39 # # 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 U48 InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(20-8)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/p+1/t6-,7+,8+/m0/s1" U48 InChIKey InChI 1.03 RGDVNLHBCKWZDA-XLPZGREQSA-O U48 SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)[NH+]=C1N" U48 SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)[NH+]=C1N" U48 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)[NH+]=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" U48 SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)[NH+]=C1N)C2CC(C(O2)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id U48 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id U48 _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site U48 "Create component" 2021-01-20 PDBE U48 "Modify atom id" 2021-01-21 PDBE U48 "Modify synonyms" 2021-03-13 RCSB U48 "Initial release" 2021-11-10 RCSB ##