data_OMC # _chem_comp.id OMC _chem_comp.name "O2'-METHYLYCYTIDINE-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 2024-09-27 _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 OMC _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 EBI _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 OMC N1 N1 N 0 1 N N N N N N 47.544 -6.422 -2.741 -0.215 -0.553 -2.308 N1 OMC 1 OMC C2 C2 C 0 1 N N N N N N 46.487 -6.797 -1.938 -0.953 0.568 -2.230 C2 OMC 2 OMC N3 N3 N 0 1 N N N N N N 45.326 -6.104 -2.002 -1.849 0.868 -3.169 N3 OMC 3 OMC C4 C4 C 0 1 N N N N N N 45.220 -5.060 -2.831 -2.045 0.059 -4.202 C4 OMC 4 OMC C5 C5 C 0 1 N N N N N N 46.306 -4.641 -3.651 -1.291 -1.127 -4.310 C5 OMC 5 OMC C6 C6 C 0 1 N N N N N N 47.440 -5.344 -3.573 -0.380 -1.415 -3.350 C6 OMC 6 OMC O2 O2 O 0 1 N N N N N N 46.638 -7.765 -1.179 -0.792 1.329 -1.290 O2 OMC 7 OMC N4 N4 N 0 1 N N N N N N 44.053 -4.404 -2.882 -2.977 0.376 -5.162 N4 OMC 8 OMC "C1'" C1* C 0 1 N N R N N N 48.763 -7.219 -2.694 0.767 -0.853 -1.263 "C1'" OMC 9 OMC "C2'" C2* C 0 1 N N R N N N 48.809 -8.221 -3.841 1.773 0.315 -1.102 "C2'" OMC 10 OMC "O2'" O2* O 0 1 N N N N N N 49.574 -9.370 -3.415 2.859 0.183 -2.022 "O2'" OMC 11 OMC CM2 CM2 C 0 1 N N N N N N 48.956 -10.355 -2.550 3.348 1.501 -2.275 CM2 OMC 12 OMC "C3'" C3* C 0 1 N N R N N N 49.502 -7.400 -4.917 2.258 0.127 0.355 "C3'" OMC 13 OMC "C4'" C4* C 0 1 N N R N N N 50.540 -6.645 -4.109 1.151 -0.715 1.016 "C4'" OMC 14 OMC "O4'" O4* O 0 1 N N N N N N 49.870 -6.354 -2.856 0.128 -0.927 0.029 "O4'" OMC 15 OMC "O3'" O3* O 0 1 N N N N N N 50.123 -8.223 -5.896 3.505 -0.570 0.381 "O3'" OMC 16 OMC "C5'" C5* C 0 1 N N N N N N 50.991 -5.353 -4.727 0.572 0.035 2.217 "C5'" OMC 17 OMC "O5'" O5* O 0 1 N N N N N N 49.863 -4.589 -5.132 -0.452 -0.753 2.823 "O5'" OMC 18 OMC P P P 0 1 N N N N N N 50.061 -3.172 -5.832 -1.013 0.092 4.073 P OMC 19 OMC OP1 O1P O 0 1 N N N N N N 48.737 -2.663 -6.280 -1.558 1.381 3.590 OP1 OMC 20 OMC OP2 O2P O 0 1 N N N N N N 51.183 -3.288 -6.804 -2.178 -0.741 4.806 OP2 OMC 21 OMC OP3 O3P O 0 1 N Y N N N N 50.576 -2.215 -4.643 0.183 0.371 5.113 OP3 OMC 22 OMC H5 H5 H 0 1 N N N N N N 46.269 -3.780 -4.339 -1.438 -1.796 -5.145 H5 OMC 23 OMC H6 H6 H 0 1 N N N N N N 48.293 -5.033 -4.198 0.209 -2.318 -3.411 H6 OMC 24 OMC HN41 1HN4 H 0 0 N N N N N N 43.972 -3.607 -3.514 -3.494 1.194 -5.085 HN41 OMC 25 OMC HN42 2HN4 H 0 0 N N N N N N 43.797 -4.107 -1.940 -3.117 -0.216 -5.917 HN42 OMC 26 OMC "H1'" H1* H 0 1 N N N N N N 48.788 -7.761 -1.720 1.291 -1.782 -1.486 "H1'" OMC 27 OMC "H2'" H2* H 0 1 N N N N N N 47.832 -8.632 -4.188 1.275 1.276 -1.226 "H2'" OMC 28 OMC HM21 1HM2 H 0 0 N N N N N N 49.546 -11.241 -2.221 4.182 1.451 -2.975 HM21 OMC 29 OMC HM22 2HM2 H 0 0 N N N N N N 48.558 -9.836 -1.646 2.551 2.110 -2.702 HM22 OMC 30 OMC HM23 3HM2 H 0 0 N N N N N N 48.015 -10.711 -3.030 3.686 1.949 -1.340 HM23 OMC 31 OMC "H3'" H3* H 0 1 N N N N N N 48.804 -6.749 -5.495 2.352 1.092 0.853 "H3'" OMC 32 OMC "H4'" H4* H 0 1 N N N N N N 51.465 -7.261 -4.021 1.558 -1.673 1.339 "H4'" OMC 33 OMC "HO3'" *HO3 H 0 0 N Y N N N N 50.556 -7.710 -6.568 3.757 -0.657 1.310 "HO3'" OMC 34 OMC "H5'" 1H5* H 0 1 N N N N N N 51.664 -4.777 -4.049 1.363 0.223 2.943 "H5'" OMC 35 OMC "H5''" 2H5* H 0 0 N N N N N N 51.707 -5.518 -5.565 0.152 0.984 1.884 "H5''" OMC 36 OMC HOP2 2HOP H 0 0 N N N N N N 51.301 -2.442 -7.221 -2.486 -0.200 5.546 HOP2 OMC 37 OMC HOP3 3HOP H 0 0 N N N N N N 50.694 -1.369 -5.060 0.509 -0.491 5.402 HOP3 OMC 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 OMC N1 C2 SING N N 1 OMC N1 C6 SING N N 2 OMC N1 "C1'" SING N N 3 OMC C2 N3 SING N N 4 OMC C2 O2 DOUB N N 5 OMC N3 C4 DOUB N N 6 OMC C4 C5 SING N N 7 OMC C4 N4 SING N N 8 OMC C5 C6 DOUB N N 9 OMC C5 H5 SING N N 10 OMC C6 H6 SING N N 11 OMC N4 HN41 SING N N 12 OMC N4 HN42 SING N N 13 OMC "C1'" "C2'" SING N N 14 OMC "C1'" "O4'" SING N N 15 OMC "C1'" "H1'" SING N N 16 OMC "C2'" "O2'" SING N N 17 OMC "C2'" "C3'" SING N N 18 OMC "C2'" "H2'" SING N N 19 OMC "O2'" CM2 SING N N 20 OMC CM2 HM21 SING N N 21 OMC CM2 HM22 SING N N 22 OMC CM2 HM23 SING N N 23 OMC "C3'" "C4'" SING N N 24 OMC "C3'" "O3'" SING N N 25 OMC "C3'" "H3'" SING N N 26 OMC "C4'" "O4'" SING N N 27 OMC "C4'" "C5'" SING N N 28 OMC "C4'" "H4'" SING N N 29 OMC "O3'" "HO3'" SING N N 30 OMC "C5'" "O5'" SING N N 31 OMC "C5'" "H5'" SING N N 32 OMC "C5'" "H5''" SING N N 33 OMC "O5'" P SING N N 34 OMC P OP1 DOUB N N 35 OMC P OP2 SING N N 36 OMC P OP3 SING N N 37 OMC OP2 HOP2 SING N N 38 OMC OP3 HOP3 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 OMC SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2OC)COP(=O)(O)O" OMC SMILES_CANONICAL CACTVS 3.341 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N" OMC SMILES CACTVS 3.341 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" OMC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" OMC SMILES "OpenEye OEToolkits" 1.5.0 "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" OMC InChI InChI 1.03 "InChI=1S/C10H16N3O8P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" OMC InChIKey InChI 1.03 USRXKJOTSNCJMA-ZOQUXTDFSA-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 OMC "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-methylcytidine 5'-(dihydrogen phosphate) ; OMC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-4-methoxy-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 OMC "Create component" 1999-07-08 EBI OMC "Modify descriptor" 2011-06-04 RCSB OMC "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id OMC _pdbx_chem_comp_pcm.modified_residue_id ARG _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 OP2 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NH1 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #