data_5MC # _chem_comp.id 5MC _chem_comp.name "5-METHYLCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 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 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 337.223 _chem_comp.one_letter_code C _chem_comp.three_letter_code 5MC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1EVV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 5MC P P P 0 1 N N N 50.109 -7.949 10.151 1.130 -0.100 -4.232 P 5MC 1 5MC OP1 O1P O 0 1 N N N 48.717 -7.449 10.362 1.708 1.219 -3.893 OP1 5MC 2 5MC OP2 O2P O 0 1 N N N 51.024 -8.102 11.312 2.287 -1.062 -4.803 OP2 5MC 3 5MC OP3 O3P O 0 1 N Y N 50.001 -9.367 9.401 -0.013 0.085 -5.351 OP3 5MC 4 5MC "O5'" O5* O 0 1 N N N 50.830 -6.988 9.102 0.487 -0.759 -2.912 "O5'" 5MC 5 5MC "C5'" C5* C 0 1 N N N 52.244 -6.857 9.086 -0.528 0.136 -2.455 "C5'" 5MC 6 5MC "C4'" C4* C 0 1 N N R 52.679 -6.121 7.845 -1.182 -0.434 -1.196 "C4'" 5MC 7 5MC "O4'" O4* O 0 1 N N N 51.896 -6.566 6.703 -0.206 -0.572 -0.140 "O4'" 5MC 8 5MC "C3'" C3* C 0 1 N N S 52.401 -4.635 7.876 -2.231 0.553 -0.637 "C3'" 5MC 9 5MC "O3'" O3* O 0 1 N N N 53.401 -3.947 8.602 -3.545 0.178 -1.056 "O3'" 5MC 10 5MC "C2'" C2* C 0 1 N N R 52.458 -4.287 6.398 -2.092 0.421 0.897 "C2'" 5MC 11 5MC "O2'" O2* O 0 1 N N N 53.767 -4.152 5.882 -3.317 -0.036 1.473 "O2'" 5MC 12 5MC "C1'" C1* C 0 1 N N R 51.743 -5.489 5.790 -0.974 -0.627 1.082 "C1'" 5MC 13 5MC N1 N1 N 0 1 N N N 50.312 -5.198 5.627 -0.131 -0.278 2.228 N1 5MC 14 5MC C2 C2 C 0 1 N N N 49.938 -4.219 4.708 0.505 0.906 2.255 C2 5MC 15 5MC O2 O2 O 0 1 N N N 50.821 -3.604 4.096 0.374 1.678 1.320 O2 5MC 16 5MC N3 N3 N 0 1 N N N 48.631 -3.956 4.514 1.277 1.249 3.285 N3 5MC 17 5MC C4 C4 C 0 1 N N N 47.714 -4.612 5.212 1.432 0.430 4.317 C4 5MC 18 5MC N4 N4 N 0 1 N N N 46.430 -4.333 4.969 2.231 0.794 5.375 N4 5MC 19 5MC C5 C5 C 0 1 N N N 48.064 -5.586 6.182 0.782 -0.821 4.318 C5 5MC 20 5MC C6 C6 C 0 1 N N N 49.363 -5.859 6.349 0.001 -1.155 3.263 C6 5MC 21 5MC CM5 CM5 C 0 1 N N N 46.991 -6.163 7.045 0.949 -1.769 5.477 CM5 5MC 22 5MC HOP2 2HOP H 0 0 N N N 51.909 -8.419 11.177 2.645 -0.632 -5.592 HOP2 5MC 23 5MC HOP3 3HOP H 0 0 N N N 50.886 -9.684 9.266 -0.362 -0.795 -5.542 HOP3 5MC 24 5MC "H5'" 1H5* H 0 1 N N N 52.629 -6.375 10.014 -1.281 0.258 -3.233 "H5'" 5MC 25 5MC "H5''" 2H5* H 0 0 N N N 52.756 -7.842 9.189 -0.082 1.104 -2.226 "H5''" 5MC 26 5MC "H4'" H4* H 0 1 N N N 53.773 -6.324 7.781 -1.646 -1.396 -1.412 "H4'" 5MC 27 5MC "H3'" H3* H 0 1 N N N 51.441 -4.358 8.372 -2.005 1.570 -0.957 "H3'" 5MC 28 5MC "HO3'" *HO3 H 0 0 N Y N 53.226 -3.013 8.621 -4.154 0.828 -0.679 "HO3'" 5MC 29 5MC "H2'" H2* H 0 1 N N N 52.005 -3.293 6.172 -1.797 1.374 1.337 "H2'" 5MC 30 5MC "HO2'" *HO2 H 0 0 N N N 53.802 -3.934 4.957 -3.987 0.631 1.272 "HO2'" 5MC 31 5MC "H1'" H1* H 0 1 N N N 52.170 -5.734 4.789 -1.403 -1.620 1.215 "H1'" 5MC 32 5MC HN41 1HN4 H 0 0 N N N 45.724 -4.837 5.505 2.683 1.653 5.369 HN41 5MC 33 5MC HN42 2HN4 H 0 0 N N N 46.243 -4.452 3.973 2.343 0.194 6.129 HN42 5MC 34 5MC H6 H6 H 0 1 N N N 49.651 -6.630 7.082 -0.509 -2.106 3.242 H6 5MC 35 5MC HM51 1HM5 H 0 0 N N N 47.266 -6.928 7.807 1.610 -1.322 6.220 HM51 5MC 36 5MC HM52 2HM5 H 0 0 N N N 46.449 -5.329 7.551 -0.023 -1.966 5.928 HM52 5MC 37 5MC HM53 3HM5 H 0 0 N N N 46.188 -6.578 6.391 1.381 -2.705 5.122 HM53 5MC 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 5MC P OP1 DOUB N N 1 5MC P OP2 SING N N 2 5MC P OP3 SING N N 3 5MC P "O5'" SING N N 4 5MC OP2 HOP2 SING N N 5 5MC OP3 HOP3 SING N N 6 5MC "O5'" "C5'" SING N N 7 5MC "C5'" "C4'" SING N N 8 5MC "C5'" "H5'" SING N N 9 5MC "C5'" "H5''" SING N N 10 5MC "C4'" "O4'" SING N N 11 5MC "C4'" "C3'" SING N N 12 5MC "C4'" "H4'" SING N N 13 5MC "O4'" "C1'" SING N N 14 5MC "C3'" "O3'" SING N N 15 5MC "C3'" "C2'" SING N N 16 5MC "C3'" "H3'" SING N N 17 5MC "O3'" "HO3'" SING N N 18 5MC "C2'" "O2'" SING N N 19 5MC "C2'" "C1'" SING N N 20 5MC "C2'" "H2'" SING N N 21 5MC "O2'" "HO2'" SING N N 22 5MC "C1'" N1 SING N N 23 5MC "C1'" "H1'" SING N N 24 5MC N1 C2 SING N N 25 5MC N1 C6 SING N N 26 5MC C2 O2 DOUB N N 27 5MC C2 N3 SING N N 28 5MC N3 C4 DOUB N N 29 5MC C4 N4 SING N N 30 5MC C4 C5 SING N N 31 5MC N4 HN41 SING N N 32 5MC N4 HN42 SING N N 33 5MC C5 C6 DOUB N N 34 5MC C5 CM5 SING N N 35 5MC C6 H6 SING N N 36 5MC CM5 HM51 SING N N 37 5MC CM5 HM52 SING N N 38 5MC CM5 HM53 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 5MC SMILES ACDLabs 10.04 "O=C1N=C(N)C(=CN1C2OC(C(O)C2O)COP(=O)(O)O)C" 5MC SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N" 5MC SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N" 5MC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 5MC SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O" 5MC InChI InChI 1.03 "InChI=1S/C10H16N3O8P/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(21-9)3-20-22(17,18)19/h2,5-7,9,14-15H,3H2,1H3,(H2,11,12,16)(H2,17,18,19)/t5-,6-,7-,9-/m1/s1" 5MC InChIKey InChI 1.03 NJQONZSFUKNYOY-JXOAFFINSA-N # 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 5MC "SYSTEMATIC NAME" ACDLabs 10.04 ;5-methylcytidine 5'-(dihydrogen phosphate) ; 5MC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-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 5MC "Create component" 1999-07-08 RCSB 5MC "Modify descriptor" 2011-06-04 RCSB #